Method for selecting personalized tri-therapy for cancer treatment

ABSTRACT

The present invention relates to a method for determining the best combinations of at least three drugs for treating cancer, which is based on the determination of the most relevant intervention points for an individual.

FIELD OF THE INVENTION

The present invention relates to the field on oncology, especially to personalized medicine in cancer therapy. More particularly, it relates a new concept of therapeutic approach, the triple regimen therapy and method for selecting the most appropriate combinations of drugs for treating cancer in a particular subject.

BACKGROUND OF THE INVENTION

Lung cancer is the most common malignancy worldwide with a staggering 1.8 million cases diagnosed per year. Over half of NSCLC are diagnosed at the metastatic stage. Even utilizing the standard of care in the Western world, consisting mainly of chemotherapeutic agents and radiation therapy, there has been little impact on mortality, with only 30% of all patients diagnosed (regardless of stage) alive at one year, and a dismal 1 and 5 year survival rates of about 8-15% and 4%, respectively for those with metastatic disease. For patients that have failed first line therapy, the median survival is only about 7 months.

Progress brought by targeted therapies such as matching EGFR activating mutations or ALK translocation have shown substantial response rates, demonstrating the potency of molecularly-matched targeted therapy, but monotherapies such as these apply to only small subsets of patients, and virtually all patients develop resistance and succumb to their disease. This is perhaps not unexpected, as patients often harbor multiple molecular aberrations that require prosecution. The power of combination therapy has been illustrated in diseases such as Hodgkin's lymphoma where cure was effected by combinations. Further in the modern era of targeted therapy, combinations targeting the same pathway (e.g. trametanib (MEK) inhibitor together with dabrafenib (BRAF inhibitor) in BRAF-mutant melanoma, or resistance pathways (combining PIK3CA and MEK inhibitors) are already being tested and have shown efficacy, in some cases, but no cure and no significant impact on survival. Combinations of targeted therapy in NSCLC have, however, to date, been very limited in scope.

Personalized medicine today offers modest benefits in advanced metastatic disease (especially lung cancer). Mono-therapies have failed to cure advanced diseases. Most combination chemotherapies lack an underlying biologic or molecular rationale.

Therefore, there is a strong need to define, for each specific patient, the best combinations of drugs for treating cancer.

SUMMARY OF THE INVENTION

The inventors present a novel concept of therapy in cancer, in particular metastatic lung cancer, based on tri therapy associating three targeted drugs. They created a simplified interventional mapping system (SIMS) merging knowledge from drugs and hallmarks of cancer. An interventional point means a target/gene, or a group of targets/genes, activated and that can be blocked by a drug. They described 24 interventional points based on a collection of 183 genes. Method of investigation of status of activation of the interventional points is based on complete genomics investigation of dual tumor and normal biopsies matched from strictly the same points, and preferably comprise sequencing, copy number variation gene expression and miRNA expression. An algorithm was developed to create a scoring system, e.g. from 1 to 10, enabling the ranking of the activated interventional points in each patient.

Based on score and trends of co-activation of interventional points, the invention presents a new scientific rationale to associate combination of therapies Accordingly, the present invention relates to a method for determining in a patient having a cancer a classification of intervention points according to their activation status, wherein

-   -   the intervention points comprise the group consisting of the         HER, CDK4,6, PLK/AURK/Kinesins, Angiogenesis, Angiopoietins,         Immune Modulators, PI3K, MET, MEK, ERK, Anti-Apoptosis, FGF,         mTOR, Ras/Raf, Telomerase, IGF/glycolysis, Wnt, PARP, HDAC,         JAK-STAT, Hedgehog, NOTCH pathway, DNA Repair and Others'         (namely RET, ALK, ROS1 and UB1), or any subgroup thereof of at         least 10 intervention points; and the genes of each intervention         point are defined according to Table 1 or 9;     -   the method comprises     -   characterizing a tumor sample in comparison to a normal         histologically matched sample from the same patient, including         -   for each pathway of the group or subgroup of intervention             points, determining the mRNA expression level of the genes             of the intervention point as disclosed in Table 1 or 9,             thereby determining a fold change of mRNA expression of             tumor vs normal, (referred as mRNA TvN fold change);         -   wholly or partially sequencing genes of Table 1 or 9,             thereby identifying the presence of activating mutation in             the tumor sample;         -   optionally, for each intervention point of the group or             subgroup of intervention points, determining the level of             miRNAs of the genes of the intervention point as disclosed             in Table 1 or 9, thereby determining a fold change of miRNAs             level of tumor vs normal, (referred as miRNA TvN fold             change);         -   optionally, for each intervention point of the group or             subgroup of intervention points, determining the copy number             variation of the genes of the intervention point as             disclosed in Table 1 or 9, thereby determining a tumor vs             normal fold change for the amplified genes;     -   calculating a score for each pathway based on the         characterization data, wherein         -   if, in the tumor sample, the presence of an activating             mutation of a gene of an intervention point is detected,             then a maximal score is given to the intervention point, in             particular a score of 10 if the scoring if from 1 to 10;         -   a score, preferably from 1 to 10, is calculated based on the             arithmetic mean of the mRNA TvN fold changes of the genes             for each intervention point of the group or subgroup of             intervention points, provided that the mRNA TvN fold change             of a gene is taken into consideration only if its value is             at least 1.3; and         -   the score of each intervention point of the group or             subgroup of intervention points is either             -   a) the sum of the score due to the presence of an                 activating mutation and the score calculated by the                 average of the mRNA TvN fold changes; or             -   b) the score due to the presence of an activating                 mutation if there is a mutation or the score calculated                 based on the arithmetic mean of the mRNA TvN fold                 changes in absence of mutation; and     -   classifying the intervention points according to the calculated         scores.

Preferably, the genes of Table 10 are sequenced for detecting the presence of mutations as defined in Table 10 and p53 gene is sequenced.

Preferably, for each intervention point of the group or subgroup of intervention points, the method comprises determining the miRNAs level of the genes of the pathway as disclosed in Table 1 or 9, in particular the level of miRNAs of the genes of the pathway as disclosed in Table 11. More preferably, before the step of score calculation, a mean miRNAs fold change for each gene is calculated as the average of the miRNA TvN fold changes for the gene, a corrected mRNA TvN fold change is calculated by dividing the mRNA fold change Tumor versus Normal of the gene (mRNA TvN fold change) by the mean fold change for the miRNAs of the gene (mean miRNA TvN fold change), and the corrected mRNA TvN fold change of the gene is then used to calculate the arithmetic mean of the mRNA TvN fold changes of the genes for each intervention point. In a preferred embodiment, the level of miRNAs is determined and used to calculate a corrected mRNA TvN fold change for the genes of the following intervention points: mTOR-AKT-PTEN, RAS, ERK, PI3K and Immune Modulators. Preferably, for each intervention point of the group or subgroup of intervention points, the method comprises determining the copy number variation of the genes of the pathway as disclosed in Table 1 or 9. More preferably, before the step of score calculation, a corrected mRNA TvN fold change of a gene of an intervention point is calculated by multiplying the mRNA TvN fold change of the gene by the CNV fold change of the gene, and the corrected mRNA TvN fold change of the gene is then used to calculate the arithmetic mean of the mRNA TvN fold changes of the genes for each intervention point.

Preferably, the subgroup of intervention points consists in the following group: Her, CDK4,6, PLK/AURK/Kinesins, Angiogenesis, Immune Modulators, PI3K, MET, MEK, ERK, Anti-Apoptosis, FGF, mTOR, Ras/Raf, IGF/glycolysis, Wnt, PARP, and DNA Repair.

Preferably, it further comprise selecting a group of three activated or disturbed intervention points in a patient having a cancer, wherein three intervention points are selected among the intervention points having the highest scores, preferably the three intervention points having the highest scores.

The present invention also relates to a method for selecting a combination of three drugs useful for treating a patient having a cancer, wherein a group of three activated or disturbed intervention points are selected by the method of claim 9 and a drug is selected for each or disturbed intervention point, thereby providing a combination of three drugs.

In addition, the present invention relates to the use of a kit for classifying pathways according to their activation status, wherein the kit comprises means for measuring the mRNA expression level of the genes of Table 1 or 9 for intervention points comprising the group consisting of the HER, CDK4,6, PLK/AURK/Kinesins, Angiogenesis, Angiopoietins, Immune Modulators, PI3K, MET, MEK, ERK, Anti-Apoptosis, FGF, mTOR, Ras/Raf, Telomerase, IGF/glycolysis, Wnt, PARP, HDAC, JAK-STAT, Hedgehog, NOTCH pathway, DNA Repair and Others' (namely RET, ALK, ROS1 and UB1), or any subgroup thereof of at least 10 intervention points. Preferably, the kit further comprises means for detecting the mutations of Table 10. More preferably, the kit further comprises means for measuring the miRNA level of miRNA of Table 11 for intervention points comprising the group consisting of the HER, CDK4,6, PLK/AURK/Kinesins, Angiogenesis, Angiopoietins, Immune Modulators, PI3K, MET, MEK, ERK, Anti-Apoptosis, FGF, mTOR, Ras/Raf, Telomerase, IGF/glycolysis, Wnt, PARP, HDAC, JAK-STAT, Hedgehog, NOTCH, DNA Repair and Others' (namely RET, ALK, ROS1 and UB1), or any subgroup thereof of at least 10 intervention points. Optionally, the kit further comprises means for determining the copy number variation of the genes of Table 1 or 9 for pathways comprising the group consisting of the HER, CDK4,6, PLK/AURK/Kinesins, Angiogenesis, Angiopoietins, Immune Modulators, PI3K, MET, MEK, ERK, Anti-Apoptosis, FGF, mTOR, Ras/Raf, Telomerase, IGF/glycolysis, Wnt, PARP, HDAC, JAK-STAT, Hedgehog, NOTCH, DNA Repair and Others' (namely RET, ALK, ROS1 and UB1), or any subgroup thereof of at least 10 intervention points.

Finally, the present invention relates to a drugs combination for use in the treatment of cancer, wherein the drugs combination is selected among the combinations disclosed in Table 6, Table 7, Table 8 or selected in the group consisting of

-   -   anti PD1L+Pan RAF inhibitor+MtorPI3K inhibitor     -   anti PD1L+Pan RAF inhibitor+angiogenesis inhibitor     -   anti PD1L+Pan RAF inhibitor+MET inhibitor     -   anti PD1L+Pan RAF inhibitor+CDK4,6 inhibitor     -   anti CTLA4+Pan RAF inhibitor+MtorPI3K inhibitor     -   anti CTLA4+Pan RAF inhibitor+angiogenesis inhibitor     -   anti CTLA4+Pan RAF inhibitor+MET inhibitor     -   anti CTLA4+Pan RAF inhibitor+CDK4,6 inhibitor     -   anti PD1L+MEK inhibitor+MtorPI3K dual inhibitor     -   anti PD1L+MEK inhibitor+angiogenesis inhibitor     -   anti PD1L+MEK inhibitor+MET inhibitor     -   anti PD1L+MEK inhibitor+CDK,-6 inhibitor     -   anti CTLA4+MEK inhibitor+MtorPI3K dual inhibitor     -   anti CTLA4+MEK inhibitor+MET inhibitor     -   anti CTLA4+MEK inhibitor+angiogenesis inhibitor, and     -   anti CTLA4+MEK inhibitor+CDK4,6 inhibitor.

Preferably, the drugs included in the combination are selected from those disclosed in Table 1.

More preferably, the drugs combination is selected in the group consisting of

-   -   Medi-4736 (Astra Zeneca)+MLN2480 (Takeda)+PF-384 (Pfizer)     -   Medi-4736 (Astra Zeneca)+MLN2480 (Takeda)+Axitinib (Pfizer) or         Motesanib (Takeda)     -   Medi-4736 (Astra Zeneca)+MLN2480 (Takeda)+Crizotinib (Pfizer)     -   Medi-4736 (Astra Zeneca)+MLN2480 (Takeda)+Palbociclib (Pfizer)     -   Tremelimumab (Astra Zeneca)+MLN2480 (Takeda)+PF-384 (Pfizer)     -   Tremelimumab (Astra Zeneca)+MLN2480 (Takeda)+Axitinib (Pfizer)         or Motesanib (Takeda)     -   Tremelimumab (Astra Zeneca)+MLN2480 (Takeda)+Crizotinib (Pfizer)     -   Tremelimumab (Astra Zeneca)+MLN2480 (Takeda)+Palbociclib         (Pfizer)     -   Medi-4736 (Astra Zeneca)+Selumetinib (Astra Zeneca)+PF-384         (Pfizer)     -   Medi-4736 (Astra Zeneca)+Selumetinib (Astra Zeneca)+Axitinib         (Pfizer) or Motesanib (Takeda)     -   Medi-4736 (Astra Zeneca)+Selumetinib (Astra Zeneca)+Crizotinib         (Pfizer)     -   Medi-4736 (Astra Zeneca)+Selumetinib (Astra Zeneca)+Palbociclib         (Pfizer)     -   Tremelimumab (Astra Zeneca)+Selumetinib (Astra Zeneca)+PF-384         (Pfizer)     -   Tremelimumab (Astra Zeneca)+Selumetinib (Astra         Zeneca)+Crizotinib (Pfizer)     -   Tremelimumab (Astra Zeneca)+Selumetinib (Astra Zeneca)+Axitinib         (Pfizer) or Motesanib (Takeda), and     -   Tremelimumab (Astra Zeneca)+Selumetinib v+Palbociclib (Pfizer).

Preferably, the cancer is a lung cancer, more preferably a NSCLC.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. The framework for cPCM. The problem is divided into 3 parts:

A. Mapping therapeutic efficacy to cellular components;

B. Scoring the status of specific nodes in the interventional maps defined in (A) and (C) predicting combination efficacy

FIG. 2. Flowchart of the scoring system.

FIG. 3. In Y: Mean fold change of differential gene expression between T and N in each patient. In X: number of patients NB: for each graph, the order of patients is different. This series serve as calibrator for calculation of deciles.

FIG. 4. Representation 3D of the scoring system. Axis Z shows score from 1 to 10. Axis X represents and example of interventional points, axis y represents each patient

DETAILED DESCRIPTION OF THE INVENTION General Concept

Since monotherapies fails to cure metastatic lung cancer diseases, and dual combinations reported today on other diseases does not imact significantly survival, the inventors envision applying tri-therapy, following the historical success in AIDS.

The challenge raised by the invention is choosing triple drug combinations that can benefit a patient.

-   -   Single drugs are doing poorly; patients respond but inevitably         relapse, often within a few months. Based on the molecular         complexity of metastatic disease, combinations are needed. This         situation may be analogous to that with AIDS, wherein single         agents resulted in incremental effects, but combination of three         drugs has demonstrated long-term benefit.     -   Unlike viruses, which always depend on the same proteins, tumors         are heterogeneous and the biology is too complex for a single         tri-therapy combination to work on all tumors.     -   As a result, combinatorial precision cancer medicine (cPCM) is         needed.     -   A limited number of pathways may be abnormal in metastatic         tumors.

The Proposed Approach

The inventors assert that, by reasonable assumptions, a realistic framework can be established today that would allow useful drug combinations to be identified in a personalized way (i.e. matching the combination to the patient based on the tumor properties).

The main idea is to divide and conquer—proposing 3 steps:

-   -   1. Find a set of markers that are indicative for specific         interventional points of every class of drugs: 24 markers         covering 183 genes     -   2. Find a score that summarizes the behavior of these markers in         a given patient that is both comparable to other classes and is         proportional to the probability that this drug would work; and     -   3. Figure out how to combine drugs such that the combination is         common enough to allow clinical testing yet we retain the         ability to match combinations to patients with sufficient         precision.

Based on these assumptions, the inventors propose the SIMS (Simplified interventional points mappins gystem) framework for precision combinational cancer medicine (FIG. 1).

-   -   First, they propose to reduce the enormous complexity of         biological pathways and pathway cross-talk by devising a         simplified map that only concentrates on the genes that are most         indicative of drug target status. They propose to define         “intervention points”, which consists of drug targets or group         of targets as well as genes upstream of the targets that         together reflect a specific biological activity that is         actionable through therapeutic interventions. For example,         pan-HER therapies define the HER group of receptors and their         ligands as a single intervention point (FIG. 1a ).     -   The second part of the work, the inventors propose a very simple         approach for prioritizing intervention points for a specific         patient. The basic premise behind the score is that, when the         genes associated with an intervention point are more disturbed         (in terms of sequence and/or expression level), the intervention         point is more likely to be crucial to the tumor. From this, it         stems that the more disturbed the genes of an intervention         point, the more likely it is that therapeutics targeted at that         points will benefit the patient. The inventors are in the         process of developing a family of simple scores that combine the         level of gene expression in the tumor (relative to matched         normal control), the aberrations found in the intervention         points' genes, CNVs and miRNAs expression levels. Rank         normalization (in the example, using deciles) is used to make         the scores of different intervention points comparable.     -   Finally, given a reliable system for determining which drugs are         more likely to benefit the patient, a method is needed for         choosing combinations that are likely to benefit the patients.         Here the inventors propose a statistical approach, using a panel         of 123 lung cancer patients as an example. Using the methods         described above, they describe the status of 24 intervention         points in the 123 patients. From this, they applied a         knowledge-driven approach to look for drug combinations that are         likely to synergistically benefit the patient. Using a panel of         experts, they identified those pathways that co-occur frequently         in the patients and are mechanistically independent. To further         improve the efficacy of the proposed combinations, the inventors         propose augmenting the combined targeted therapies with         immunomodulating therapies (i.e. anti-CD1L and anti-CTLA). The         rational behind this combination is to reduce the chance of         intolerable side effects while maintain the predicted efficacy         of a triple therapy regimen

Drugs acting on Interventional interventional node Components of the inteventional points points HER EGF, TGFA, AREG, EREG, HBEGF, BTC, NRG1, Dacomitinib-Panher NRG2, NRG4, EGFR, ERBB2, ERBB3, ERBB4 inhibitor Pfizer CDK4, 6 CDK4, CDK6, CCND1, CCND2, CCND3, Palbociclib CDK4, 6 CDKN2A, CDKN2B, CCNE1, CCNE2, CCNE3, RB1 inhibitor Pfizer PLK/ PLK1, AURKA, BORA, ILK, KIF11 MLN8237 (Aurora A AURK/Kine kin inhib) Takeda ANGIOGENESIS VEGFA, VEGFB, VEGFC, VEGFD, VEGFR1, VEGFR2, Axitinib antiVEGFR VEGFR3, PDGFA, PDGFB, PDGFRA, PDGFRB, Kit Pfizer Motesanib anti VEGFR/PDGFR/kit Takeda Angiopoietins THBS1, TGFB1, ANGPT1, ANGPT2, ANGPTL1, — ANGPT4, TIE1, TEK Immune mod PD1L, PDCD1LG2, PDCD1, CTLA4, LAG3 Medi-4736 (PDL1) AZ (Astra Zeneca) AMP514 (PD1) AZ Tremelimumab (CTLA4) AZ PF-05082566 (4-1 BB) PI3K PIK3CA, PIK3CB, PIK3CD, PIK3CG, PIK3C2B, PRKCB, PF-384 PI3K/mTOR- PRKCA, PRKCB, PIK3R1, PIK3R2, PIK3R3 inhibitor Pfizer AZD8186 (PI3Kb)AZ MLN1117 (PI3Kalpha inhibitor) Takeda MET HGF, MET, AXL, MST1R Crizotinib Pfizer Volitinib (cMet) AZ MLN1117, MLN0128 Takeda MEK MAP2K1, MAP2K2, MAP2K3, MAP2K4, MAP3K1, Selumetinib (MEK) MAP3K2, MAP3K3, MAP3K4 AZ ERK MAPK3, MAPK1, KSR1, MAPK11 — Anti-apoptosis BCL2, BCLXL, BIRC5, XIAP, BAK1, TP53 — FGF FGF1 to FGF18, FGFR1, FGFR2, FGFR3, FGFR4 AZD4547 (FGFR1, 2, 3) AZ mTOR mTor, AKT1, AKT2, PTEN, PF-384 PI3K/mTOR TSC1, TSC2, STK11, PIM1, PIM2, PIM3 inhibitor Pfizer AZD2014 (TOR kinase) AZ AZD5363 (AKT1, 2, 3) AZ AZD1208 (PIM1, 2) AZ MLN0128 (TORC1/TORC2) Takeda Ras/Raf KRAS, NRAS, HRAS, RAF1, BRAF, CRAF MLN2480 (Pan-RAF inhibitor) Takeda Telomerase TERT, TERC, TEP1, HSP90AA1, DKC1, PTGES3 — IGF/glycolysis IGF1, IGF2, IGF1R, IGF2R, INSR, IRS1, PKM Medi-573 (IGF) AZ Wnt CDH1, CTNNA1, CTNNB1, WNT 1, FZD1, WNT5A, B, — FZD5, WIF1, DKK1 PARP PARP1, BRCA1, XRCC1, RAD54L, RAD54B, ATM, Olaparib (PARP) AZ ATR, CHEK1, CHEK2, WEE1 AZD1775 (Wee1) AZ AZD6738 (ATR) AZ HDAC HDAC1, HDAC2, HDAC3, HDAC4, HDAC5 JAK-STAT JAK1, JAK2, STAT1, STAT2, STAT3, SOCS1 Hedgehog SHH, PTCH1, SMO, STK36, PRKACA, SUFU, GLI1 NOTCH NOTCH1, Adam17, PSEN1, NCSTN, JAG1, SRRT, APH1A DNA Repair ERCC1, RAD52, XRCC4, RAD51, BRCA1, NEDD8, NAE1 MLN 4924 (NEDD8 AE) Takeda Others RET, ALK, ROS1, UB1

CONCLUSION

The inventors propose a new therapeutic approach of triple regimen therapies aiming at blocking simultaneously three different biologic abnormalities and reducing the chance of developing the secondary resistance. In addition, for defining a combination of drugs, the inventors identified specific interventional points of drugs based on the pathways specifically up-regulated in one particular patient having a cancer. They defined a simplified interventional mapping system within the hallmarks of cancer including only signaling and regulatory pathways that can be targeted with therapeutic agents. The principle of simplification is based on the activating signal that can be blocked by a class of drugs. Indeed, the inventors reduce the enormous complexity of biological pathways and pathway cross-talk by devising a simplified map that only concentrates on the gens that are most indicative of drug target status defined as “intervention points”. These intervention points consist of drug targets or group of drug targets and some genes upstream of the drug targets that together reflect a specific biological activity which is actionable through therapeutic interventions. By upstream is referred to genes encoding a protein having an extracellular activity. For instance, pan-HER therapies define the HER group of receptors and their ligands as a single intervention point.

The inventors propose a very simple approach for prioritizing intervention points for a specific patient. The basic premise is that, when the genes associated with an intervention point are more disturbed (in terms of sequence and/or expression level), the intervention point is more likely to be crucial or critical to the tumor. From this, it stems that the more disturbed the genes of an intervention point are, the more likely it is that therapeutics targeting that points will benefit the patient. Accordingly, the inventors have developed a family of simple scores that combine the level of gene expression in the tumor (relative to matched normal control), the mutations found in the intervention points' genes, CNVs and miRNAs expression levels.

Therefore, the inventors propose a method allowing the tumor characterization of one particular subject by considering its own tumor vs normal status in the most efficient way for identifying the disturbed or activated intervention points and ranking them. The inventors developed a new mathematical modelling and scoring system to give a score (e.g., of 1 to 10) based on integration of omics data, especially gene expression, sequencing, miRNA analysis and copy number variation determination.

Then, when the intervention points are ranked, it is possible to define one or several combinations of drugs targeting a combination of disturbed or activated intervention points so as to obtain the optimized therapy of cancer for this particular patient. Preferably, the combined therapy comprises or consists of three drugs targeting the most disturbed or activated intervention points. The method may further comprise the administration of the optimized combination of drugs to said patient. Accordingly, the method leads to rational combination therapies which are scientifically reliable and clinically feasible.

Tumour Characterization

The method comprises a step of characterizing the tumor in one patient of interest. In particular, the patient suffers from a cancer for which no effective therapy is established or admitted by physicians. The reasons of this situation could be an advanced stage of cancer, for instance a stage with metastases, a relapsed cancer after one or several lines of treatment, or even a cancer for which no established and efficient treatment is associated with. In particular, the cancers or tumors more particularly considered in the present invention are lung cancer, especially NSCLC (non-small cell lung cancer), breast cancer (in particular the triple negative breast cancer), colorectal cancers, kidney cancer, melanomas, brain cancers, liver cancers, head and neck cancers, stomach cancers and ovary cancers. Therefore, the method comprises an initial step of providing samples for the patient. Two samples are necessary, namely one tumor sample and one normal sample from the same patient. Preferably, the tumour sample and the normal sample provides from the same type of tissue. More particularly, the tumor and normal samples are histologically matched tissues. Typically, the samples can be provided by biopsies. Non-exhaustively, examples of pairs of tumor with corresponding histological normal reference tissue are the followings:

-   -   1. lung cancer adenocarcinomas or derived metastases—bronchial         normal mucosa     -   2. breast cancer tumors or derived metastases—normal epithelial         breast cells     -   3. colon cancers adenocarcinomas or derived metastases—normal         colon mucosa     -   4. kidney cancers or derived metastases—normal kidney cells     -   5. melanomas or derived metastases—synchronous naevi     -   6. rhabdomyosarcomas or derived metastases—normal muscle tissue     -   7. liver carcinomas or derived metastases—normal liver cells     -   8. Oral-pharyngeals tumors (ORL)—normal buccal mucosa     -   9. Stomach carcinomas or derived metastases—normal stomach         mucosa     -   10. Ovary cancer—normal Fallope tube mucosa     -   11. pancreatic cancers—normal parenchimatous tissue from         pancreas

In order to optimize the tumor characterization, the inventors selected parameters that have to be analysed in order to establish the status of the intervention points that can be targeted by a class of drugs.

The inventors defined the main intervention points of interest, namely HER (Human Epithelial Growth Factor Receptor), CDK4,6 (Cyclin-Dependent Kinase), PLK/AURK/Kinesins (Polo-Like kinase/Aurora Kinase/Kinesins), Angiogenesis, Angiopoietins, Immune Modulators, PI3K (Phosphoinositide-3 Kinase), MET (cMET), MEK, ERK, Anti-Apoptosis, FGF (Fibroblast Growth Factor), mTOR (mammalian target of rapamycin), Ras/Raf, Telomerase, IGF/glycolysis (Insulin-like growth factor), Wnt, PARP (poly ADP ribose polymerase), HDAC (histone deacetylase), JAK-STAT (Janus tyrosine Kinase-Signal Transducer and Activator of Transcription), Hedgehog, NOTCH, DNA Repair and Others' intervention point (namely RET, ALK, ROS1 and UB1). These intervention points have been selected because they can be associated with an activation in a cancer. The rule that guides the choice of the invention in this selection is to select the activation signals that can be blocked.

Optionally, in an alternative method, a subgroup of intervention points can be selected among the above mentioned list of intervention points (i.e., a subgroup of 10, 12, 14, 16 or 18 intervention points). For instance, in a particular embodiment, a subgroup of intervention points of interest includes the intervention points for which drugs are available. For instance, such a subgroup may include or consist in the following group: Her, CDK4,6, PLK/AURK/Kinesins, Angiogenesis, Immune Modulators PD1L and CTL14, PI3K, MET, MEK, ERK, Anti-Apoptosis, FGF, mTOR, Ras/Raf, IGF/glycolysis, Wnt, PARP, and DNA Repair.

In addition, for each intervention point, the inventors carried out a selection of genes useful for characterizing this intervention point. The list of genes is disclosed in Table 1 or 9.

In order to define the status of these intervention points in the tumor, several parameters have to be defined based on the limited list of genes that need to be investigated for each patient.

In a first aspect, expression levels of the genes of Table 1 or 9 are determined in the tumor and normal samples. The expression levels are determined by measuring mRNA level. The determination of the expression level variation for these mRNA is carried out by comparing the expression levels in a tumor tissue and in the corresponding normal tissue. The gene expression analysis allows the study of independent deregulations or deregulations due to chromosomal aberrations. Indeed, the regulation of the transformational activity of genes is complex and involves many levels of regulation: trans/cis transcription factors, promoters, chromatin regulation, and the like. Generally, all deregulations (over-expression) are considered with a ratio tumour/normal of at least 1.3. For each deregulated gene (i.e., gene with a different mRNA expression when tumor and normal samples are compared), a fold change and/or intensity of signal (proportional to the mRNA expression level) is determined. Technologies that can be used comprise Northern analysis, mRNA or cDNA microarrays, RT-PCT (in particular quantitative RT-PCR) and the like. Alternatively, the level of expression can be determined with a ship comprising a set of primers or probes specific for the list of genes of Table 1 or 9 or a set specific of genes of a subgroup of 10, 12, 14, 16 or 18 intervention points as disclosed in Table 1 or 9. Expression levels obtained from cancer and normal samples may be normalized by using expression levels of proteins which are known to have stable expression such as RPLPO (acidic ribosomal phosphoprotein PO), TBP (TATA box binding protein), GAPDH (glyceraldehyde 3-phosphate dehydrogenase) or β-actin.

It is important to note that the method according to the present invention is clearly distinct from a method of global or whole analysis of gene expression. Even if some genes can be added to the list of genes of Table 1 or 9, the gene expression is determined for less than 200, 250, or 300 genes.

In a second aspect, some genes of the list of genes of Table 1 and 9 are analyzed by sequencing (partial or whole sequencing) or by hybridization for detecting the presence or absence of mutations. For instance, exons of the genes of Table 1 or 9 can be sequenced by any method available, preferably by a method of high throughput sequencing such as Illumina or Ion Torrent method or equivalent. Alternatively, only genes with known activating mutation(s) can be analyzed. Such list of genes and mutations can change depending on the considered cancer. In a particular embodiment, the genes of Table 10 can be analyzed for the presence of mutations. More preferably, the method includes the sequencing of p53, the most frequent mutated gene in solid tumors. For instance, the method may include the determination of the presence/absence of mutations in the genes p53, KRAS or NRAS (preferably KRAS), EGFR, EBBR2, PIK3CA and BRAF. Indeed, the presence of mutation leading to a functional gain or loss has an important effect on biology of the tumour without being always connected to variations of gene expression or of gene copy number. Many mutations are known to have a direct effect on the activity of a treatment by inducing increased sensitivities or resistances. For example, the mutations in the tyrosine kinase domain of EGFR are often associated with sensitivity to the small molecules inhibiting EGFR, the mutations in KRAS gene are associated with resistance to the treatment by monoclonal antibodies targeting EGFR. The mutational status can be determined by any method known in the art, for instance by sequencing, microsequencing or hybridization. In addition, the gene mutations are listed in in www.sanger.ac.uk/genetics/CGP/cosmic/.

In a third aspect, the copy number variation of genes are defined for the tumor sample of the subject. This analysis can be carried out by CGH (Comparative Genomic Hybridization) which makes it possible to compare the tumor DNA with the normal DNA of the same individual to detect chromosomal aberrations, i.e. copy number variation such as chromosomal losses or gains. This technology is well-known by the man skilled in the art. As an illustration of this knowledge, the following reviews or reference books can be cited: Davies et al. (2005, Chromosome Research, 13, 237-248). This technology is useful to identify translocations. It can be easily carried out with frozen biopsies or tumor paraffin-included material. CGH results are expressed as the ratios of copy numbers in the tumor material and in normal tissue. A threshold of 0.5 is been acknowledged to describe a gain or a loss. More this ratio is high, more the amplitude of the anomaly is important. Thus, an important anomaly is likely to have a real impact at the biological level. In a preferred embodiment, a fold change of the copy number variation is determined.

In a fourth aspect, levels of miRNAs or microRNAs for the genes of Table 1 or 9 are determined in the tumor and normal samples. More preferably, the levels of 5 miRNAs for each gene is determined. In a preferred embodiment, the miRNAs of Table 11 are analyzed. The method for measuring miRNA are well-known in the art.

Then, a fold change Tumor versus Normal tissue is determined for the 5 miRNAs and a mean fold change for each gene is calculated as the average of the fold changes of the 5 miRNAs.

Then, after the characterization step, the following parameters for the tumor of each specific patient have been determined:

-   -   A list of genes among the list of Table 1 or 9 with a         deregulated expression with a defined fold-change.     -   A list of mutated genes.     -   Optionally, a list of genes having a Copy Number Variation and a         value (fold-change) for this CNV. In a preferred embodiment,         only the genes presenting an amplification are taken into         consideration.     -   Optionally, a list of deregulated miRNA, in particular with an         averaged fold change based on the 5 miRNA fold-change.

In a first embodiment, the characterization method includes the gene expression analysis and the mutated genes. In a second embodiment, the characterization method includes the gene expression analysis, the mutated genes and the Copy Number Variation. In a third embodiment, the characterization method includes the gene expression analysis, the mutated genes and the miRNA analysis. In a fourth embodiment, the characterization method includes the gene expression analysis, the mutated genes, the Copy Number Variation and the miRNA analysis. The choice of the combination of criteria can be different for each intervention point.

For instance, for some intervention points, the impact of miRNA has a major influence whereas for other intervention points, miRNA has a minor influence. As shown in the example section, for patients having NSCLC, miRNAs have a major impact on the intervention points mTOR-AKT-PTEN, RAS, ERK, PI3K and Immune Modulators, whereas the impact is minor for the intervention points Her, CDK4,6, Angiogenesis, MET, MEK, FGFR, RAF, IGF-Warburg, and PARP. In addition, for patients having NSCLC, the impact of CNV has been determined as quite low.

From these parameters, the method comprises that determination of the disturbed or activated intervention points in the tumor of the patient and the ranking of them by calculating a score for each intervention point.

Mathematical Modeling/Algorithm

The principles of the algorithm for calculating a score for each intervention point are the followings:

-   -   1—The score is designed to correlate with the likelihood that an         intervention point is (abnormally) activated or disturbed in the         tumor, in particular in comparison to the normal matched tissue         of the same patient. It ranges from 1 to 20, the highest is the         score, the most activated or disturbed is the pathway. In a         preferred embodiment, the score ranges from 1 to 10. However,         the scale of the score has no impact on the results.     -   2—The score may combine evidence from 4 data sources:         -   Mutations;         -   Mean fold change in gene differently expressed in the tumor             vs. normal;         -   Optionally, Mean fold change in expression of miRNA of tumor             vs. normal; and,         -   Optionally, Copy number variation.

Activating Mutation and the Score Calculation

The different data sources may carry different weights in the score. Indeed, activating mutation (e.g. K-RAS in the RAS pathway) may have decisive weight.

Then, in a first approach of the method, the maximal score is given to each intervention point comprising a gene with an activating mutation. In a preferred embodiment, the mutations associated with a maximal score are listed in Table 10. It may further include the p53 mutations. For instance, if the score ranges from 0 to 10, the maximal score of 10 is given to every intervention point comprising a gene with an activating mutation. In the absence of a mutation, the score is based on an average of the mRNA mean fold changes, optionally weighted with the level of expression of miRNAs and to a lesser extent CNV abnormalities.

In a second approach, the rules of the first approach are carried out, but the score is the sum of two scores, a first one based on mutation and a second one based on the arithmetic mean of the mRNA mean fold changes. Preferably, the range/scale of the two scores is the same. For instance, the two scores each range from 0 to 10.

In a third approach, the score is the sum of two scores, a first one based on mutation and a second one based on the mRNA mean fold change. However, a different weight/score can be given to mutations. In particular, instead of giving a score of 10 as soon as an activating mutation is detected, a lower score can be given to the activating mutation, for instance a score of 3. Accordingly, one mutation in a gene of an intervention point gives a score of 3, two mutations a score of 6, three mutations a score of 9, more mutations the maximal score of 10. In addition, depending on the impact of the activating mutations, a different weight can be given. For instance, an activating mutation of KRAS gives a score of 10, whereas a mutation with less functional impact will count for 3. Accordingly, mutations listed in Table 10 may have a higher weight, for instance may count 10.

Calculating the Mean Fold-Change of Differentially Expressed Genes:

The global expression pattern is used to calculate a fold-change (f_(i)) of the expression of a gene i in the tumor and in the matched normal tissue. This fold change can be referred as mRNA TvN fold change. It is calculated as the ratio of the expression of a gene in tumor on the expression of the gene in a normal tissue.

For calculating the mean/average fold change of intervention point k, denoted as E_(k), the fold changes of differentially expressed genes with a fold change of at least 1.3 are used. In other words, for each intervention point, an average fold-change of the genes i of the intervention point k is calculated, trimming values with a threshold of ≦1.3.

Formally, we calculate E_(k) as the following: let M_(k) denote the set of genes that belong to intervention point k, and m_(k) denote the subset of M_(k) that includes only differential expressed genes with an absolute fold change ≧1.3. E_(k) is the average of the fold change of the genes m_(k).

m _(k) ={i|iεM _(k) and |F _(E)>1.3}

We then calculate the mean expression level for all the genes in m_(k):

E _(k) =F _(l) wherein iεm _(k)

In other words, the fold change for a particular intervention point is the average or arithmetic mean of the fold changes of genes belonging to the intervention point as defined in Table 1 or 9 and having a fold change T vs N of 1.3 or more.

In particular, in order to compare the fold changes of different intervention points, a relative scoring, e.g., from 1 to 10, is generated based on the percentile calculation.

Combining mRNA and miRNA Measurements

To adjust for possible miRNA intervention in translation, the inventors propose to penalize discordance between miRNA and its target mRNA. For each of the genes of Table 1 or 9 that belong to the intervention points or a set thereof, the inventors determined the miRNAs most likely to be involved in their regulation using Target scan {http://www.targetscan.org/}, selecting the top 5 miRNAs for each gene. Table 11 provides a list of the top 5 miRNAs for the genes of Table 1 or 9.

For each gene i, a mean miRNA fold-change can be calculated, which is denoted A_(i), by averaging the fold changes of the 5 miRNAs (or less if less than 5 miRNAs are identified) that are most likely to target gene i. Then, for each gene, a mean miRNA TvN fold change is determined.

Then, a corrected fold change of a gene of an intervention point is calculated by dividing the mRNA fold change Tumor versus Normal of the gene (mRNA TvN fold change) by the mean fold change for the miRNAs of the gene (mean miRNA TvN fold change). The corrected fold change of a gene is then used to calculate the fold change for a particular pathway by using it in the calculation of the average fold changes of the genes belonging to the pathway as defined in Table 1 or 9 and having a fold change T vs N of 1.3 or more. Based on the corrected fold change of pathways, a corrected score, e.g., a score 1 to 10 is generated based on percentiles.

Combining mRNA and CNV Measurements

Only genes with amplification are taken into account. Preferably, genes with 2-fold or higher amplification are considered as amplified. Then, a corrected fold change of a gene of an intervention point is calculated by multiplying the mRNA fold change Tumor versus Normal of the gene (mRNA TvN fold change) by the CNV fold change of the gene. The corrected fold change of a gene is then used to calculate the fold change for a particular intervention point by using it in the calculation of the average fold changes of the genes belonging to the intervention point as defined in Table 1 or 9 and having a fold change T vs N of 1.3 or more. Based on the corrected fold change of pathways, a corrected score, e.g., a score 1 to 10 is generated based on percentiles.

Score Calculation

To compare intervention points, a score is given to each intervention point, taking into account mRNA expression and activating mutation. Optionally, 3 or 4 variables can be considered: activating mutations, the Fold change of mRNAs in Tumor vs. Normal, the fold change of miRNAs in Tumor vs. Normal and the copy number variation (amplifications, deletions). In a preferred embodiment, the score is given to each intervention point, taking into account activating mutations, mRNA expression, and miRNA expression. In a particular embodiment, the miRNA is considered when calculating the score at least for the following intervention points: mTOR-AKT-PTEN, RAS, ERK, PI3K and Immune Modulators.

To summarize, in a first aspect, the score for each pathway is calculated as follow:

-   -   1—If an activating mutation is detected in one gene of the         intervention point, then the score of the intervention point is         the maximal score, e.g. 10 when scoring from 1 to 10.     -   2—Otherwise, the score is calculated based on the average of the         fold changes tumor vs normal of the genes having an absolute         fold change of at least 1.3 and belonging to the list of genes         of Table 1 or 9 for the considered intervention point.     -   3—Optionally, if the miRNA level of the genes of Table 1 or 9 is         measured, in particular those of Table 11, a mean miRNA fold         change for each gene is calculated as the arithmetic mean of the         fold change of 5 miRNAs of this gene. Then a corrected mRNA fold         change for the gene is calculated by dividing the mRNA fold         change Tumor versus Normal of the gene (mRNA TvN fold change) by         the mean fold change for the miRNAs of the gene (mean miRNA TvN         fold change). For calculating the mean of the mRNA tumor vs         normal fold changes of the genes of an intervention point, the         corrected mRNA TvN fold change for the gene is used.     -   4—Optionally, if the CNV of the genes of Table 1 or 9 (or some         genes thereof) is measured with 2-fold or higher amplification,         then a corrected mRNA fold change for the gene is calculated by         multiplying the mRNA fold change Tumor versus Normal of the gene         (mRNA TvN fold change) by the CNV fold change for the gene. For         calculating the mean of the mRNA tumor vs normal fold changes of         the genes of an intervention point, the corrected mRNA TvN fold         change for the gene is used.

Alternatively, it can also be chosen to attribute less weight to mutations, in particular when considering the sequencing of all genes of Table 1 or 9. Accordingly, in a first alternative, the score is the sum of the score due to mutational status and the score due to the mRNA differential TvN expression. In a second alternative, in order to graduate the impact of the mutations, a score of 3 is given by activating mutation. Then, for instance, the score of a pathway is a score based on activating mutations with a maximal score of 10 added to a score based on mRNA expression is calculated above with a maximal score of 10. Accordingly, for each intervention point, the score will be comprised between 0 and 20.

Based on the scores of the intervention points, the intervention points are ranked. The pathway ranking can allow the one skilled in the art to select one or several combinations of three activated or disturbed intervention points, especially the combination of the three most activated or disturbed intervention points according to the scores.

The pathways have been selected because drugs specific to each intervention point are already or soon available for treating a patient (see Table 1). Accordingly, based on the combination of selected intervention points, a combination of drugs targeting these intervention points can be selected and proposed for treating the patient.

Therefore, the present invention relates to a method for selecting a combination of three drugs useful for treating a patient having a cancer, wherein a group of three activated or disturbed intervention points are selected by the method of the present invention and a drug is selected for each activated or disturbed intervention point, thereby providing a combination of three drugs.

Prior any administration to a patient, the efficacy of the drugs combination can be tested ex vivo. For instance, the combination can be tested on a model based on a biopsy of the tumor from the patient. It can be tested on an animal model on which tumor cells from the tumor has been grafted. Alternatively, it can be tested in a pre-clinical model called Metastatic Ex Vivo Assay (MEVA). It is an in vitro 3D tissue culture through an anchorage independent system.

Then, the present invention relates to a method of treatment of a patient having a cancer or a method for selecting a combination of drugs for treating a patient having a cancer, comprising:

-   -   Providing a tumor sample and an histologically matched normal         tissue from the patient;     -   Characterizing the tumor sample in comparison to the normal         sample as detailed above;     -   Calculating a score for each intervention point as detailed         above;     -   Selecting three activated or disturbed intervention points,         preferably the three most activated or disturbed intervention         points;     -   Selecting a combination of drugs targeting the three selected         activated or disturbed intervention points;     -   Optionally, administrating to the patient the selected         combination of drugs.

Optionally, the method of the present invention can provide several combinations of three drugs. Indeed, in order to prevent any drug resistance, the combinations can be used sequentially.

In addition, the present invention relates to a kit and the use of such a kit for classifying intervention points according to their status and for selecting a combination of three drugs chosen as targeting the most activated or disturbed intervention points, wherein the kit comprises means for measuring the mRNA expression level of the genes of Table 1 or 9. In particular, such means can be primers and/or probes specific for each gene of Table 1 or 9. Optionally, the kit may further comprise means for detecting the mutations in genes of Table 1 or 9. These means could be suitable for the whole sequencing of the genes of Table 1 or 9. More preferably, the kit comprises means for detecting the mutations of Table 10. Means can be probes specific of the nucleic acid sequence encoding a fragment including the mutation. They can also be primers allowing the amplification and sequencing of the genes. Optionally, the kit may further comprise means for determining the level of miRNA of genes of Table 1 or 9, in particular those of Table 11. Finally, the kit may further comprise means for determining the copy number variation of the genes of Table 1 or 9.

Finally, the present invention relates to drugs combinations of interest identified by the method of the present invention. In a particular embodiment, the present invention relates to a drugs combination including one drug targeting PDL1 or CTLA4 and two drugs selected from the group consisting of an inhibitor of RAF, an inhibitor of Angiogenesis, an inhibitor of MEK; an inhibitor of MET and an inhibitor of CDK 4,6.

The main reason to define triple regiment therapies as a combination of an immunomodulator (anti PD1L or anti CTLA4) and two targeted therapies is to contain toxicity of associations. Indeed, the main problem of combining targeted therapies might be the additive toxicity. Whilst containing toxicity of dual combination was already demonstrated, adding a third drug such as anti PD1L may contribute to an effective tolerated therapy, in particular for metastatic NSCLC.

Accordingly, the present invention relates to a drugs combination for use in the treatment of cancer, wherein the drugs combination is selected among the combinations disclosed in Table 6, Table 7, Table 8.

Preferably, the drugs combination is the combination of three drugs. Optionally, it may include additional drugs.

In a more specific embodiment, the present invention relates to a drugs combination including a drug targeting PDL1, an inhibitor of RAF and a third targeted drug such as an inhibitor of MEK6, an inhibitor of MET, an inhibitor of CDK4,6 or an inhibitor of angiogenesis. Based on analysis of frequency of occurrence of activated interventional points, and based on analysis of trends of co-activation, the most important combinations are the following:

-   -   1. anti PD1L (e.g., AZ)+Pan RAF inhibitor (e.g.,         Takeda)*+MtorPI3K inhibitor (e.g., Pfizer)     -   2. anti PD1L (e.g., AZ)+Pan RAF inhibitor (e.g.,         Takeda)*+angio-inhibitor (e.g., Pfizer)     -   3. anti PD1L (e.g., AZ)+Pan RAF inhibitor (e.g., Takeda)*+met         inhibitor (e.g., Pfizer)     -   4. anti PD1L (e.g., AZ)+Pan RAF inhibitor (e.g., Takeda)*+CDK4,6         inhibitor (e.g., Pfizer)         these for combinations covers 51% of patients with NSCLC as         determined in the analysis of the retrospective collection of         123 patients.

In addition to these 4 combinations, the inventors determined that replacing PD1L with CTL14 fulfils the criteria of combining an immunomodulator with two others targeted drugs. Four additional combinations can be envisioned, increasing the coverage of patients to 72%

-   -   5. anti CTLA4 (e.g., AZ)+Pan RAF inhibitor (e.g.,         Takeda)*+MtorPI3K inhibitor (e.g., Pfizer)     -   6. anti CTLA4 (e.g., AZ)+Pan RAF inhibitor (e.g.,         Takeda)*+angio-inhibitor (e.g., Pfizer)     -   7. anti CTLA4 (e.g., AZ)+Pan RAF inhibitor (e.g., Takeda)*+met         inhibitor (e.g., Pfizer)     -   8. anti CTLA4 (e.g., AZ)+Pan RAF inhibitor (e.g.,         Takeda)*+CDK4,6 inhibitor (e.g., Pfizer)

It is worthwhile to mention that the Pan RAF inhibitor could be replaced with a MEK inhibitor in most of the patients. This replacement generates 8 combinations:

-   -   9. anti PD1L (e.g., AZ)+MEK inhibitor+MtorPI3K dual inhibitor         (e.g., Pfizer)     -   10. anti PD1L (e.g., AZ)+MEK inhibitor+angio-inhibitor (e.g.,         Pfizer or Takeda)     -   11. anti PD1L (e.g., AZ)+MEK inhibitor+met inhibitor (e.g.,         Pfizer)     -   12. anti PD1L (e.g., AZ)+MEK inhibitor+CDK,-6 inhibitor (e.g.,         Pfizer)     -   13. anti CTLA4 (e.g., AZ)+MEK inhibitor+MtorPI3K dual inhibitor         (e.g., Pfizer)     -   14. anti CTLA4 (e.g., AZ)+MEK inhibitor+metinhibitor (e.g.,         Pfizer)     -   15. anti CTLA4 (e.g., AZ)+MEK inhibitor+angio_inhibitor (e.g.,         Pfizer or Takeda)     -   16. anti CTLA4 (e.g., AZ)+MEK inhibitor+CDK4,6 inhibitor (e.g.,         Pfizer)

In a preferred embodiment, the above-mentioned drugs can be selected among those disclosed in Table 1.

More preferably, the drugs combination is selected in the group consisting of

-   -   Medi-4736 (Astra Zeneca)+MLN2480 (Takeda)+PF-384 (Pfizer)     -   Medi-4736 (Astra Zeneca)+MLN2480 (Takeda)+Axitinib (Pfizer) or         Motesanib (Takeda)     -   Medi-4736 (Astra Zeneca)+MLN2480 (Takeda)+Crizotinib (Pfizer)     -   Medi-4736 (Astra Zeneca)+MLN2480 (Takeda)+Palbociclib (Pfizer)     -   Tremelimumab (Astra Zeneca)+MLN2480 (Takeda)+PF-384 (Pfizer)     -   Tremelimumab (Astra Zeneca)+MLN2480 (Takeda)+Axitinib (Pfizer)         or Motesanib (Takeda)     -   Tremelimumab (Astra Zeneca)+MLN2480 (Takeda)+Crizotinib (Pfizer)     -   Tremelimumab (Astra Zeneca)+MLN2480 (Takeda)+Palbociclib         (Pfizer)     -   Medi-4736 (Astra Zeneca)+Selumetinib (Astra Zeneca)+PF-384         (Pfizer)     -   Medi-4736 (Astra Zeneca)+Selumetinib (Astra Zeneca)+Axitinib         (Pfizer) or Motesanib (Takeda)     -   Medi-4736 (Astra Zeneca)+Selumetinib (Astra Zeneca)+Crizotinib         (Pfizer)     -   Medi-4736 (Astra Zeneca)+Selumetinib (Astra Zeneca)+Palbociclib         (Pfizer)     -   Tremelimumab (Astra Zeneca)+Selumetinib (Astra Zeneca)+PF-384         (Pfizer)     -   Tremelimumab (Astra Zeneca)+Selumetinib (Astra         Zeneca)+Crizotinib (Pfizer)     -   Tremelimumab (Astra Zeneca)+Selumetinib (Astra Zeneca)+Axitinib         (Pfizer) or Motesanib (Takeda), and     -   Tremelimumab (Astra Zeneca)+Selumetinib v+Palbociclib (Pfizer).

By a “drugs combination”, it is referred to a pharmaceutical composition comprising the drugs of the combination or to a kit or product comprising the drugs of the combination as a combined preparation for simultaneous, separate or sequential use.

The present invention relates to

-   -   a pharmaceutical composition comprising the drugs of the         combination, and a pharmaceutically acceptable carrier, in         particular for use in the treatment of cancer; and/or     -   a product or kit containing the drugs of the combination, as a         combined preparation for simultaneous, separate or sequential         use, in particular in the treatment of cancer; and/or     -   a combined preparation which comprises the drugs of the         combination, for simultaneous, separate or sequential use, in         particular in the treatment of cancer; and/or     -   a pharmaceutical composition comprising the drugs of the         combination for the use in the treatment of cancer in         combination with radiotherapy and/or or an additional         anti-tumoral agent; and/or     -   the use of a pharmaceutical composition comprising the drugs of         the combination for the manufacture of a medicament for the         treatment of cancer; and/or     -   the use of a pharmaceutical composition comprising the drugs of         the combination for the manufacture of a medicament for the         treatment of cancer in combination with radiotherapy, and/or or         an additional anti-tumoral agent; and/or     -   a method for treating a cancer in a subject in need thereof,         comprising administering an effective amount of a pharmaceutical         composition comprising the drugs of the combination, and a         pharmaceutically acceptable carrier; and/or     -   a method for treating a cancer in a subject in need thereof,         comprising administering an effective amount of the drugs of the         combination; and/or     -   a method for treating a cancer in a subject in need thereof,         comprising administering an effective amount of a pharmaceutical         composition comprising the drugs of the combination in         combination with radiotherapy.

In a preferred embodiment, the cancer is a lung cancer, and more preferably a NSCLC.

The following chapter, describes material, methods and results presenting full investigation of possibilities of combinations, based on magnitude and frequency of occurrence of interventional points of activation as determined by the scoring system. In addition, selection of combinations takes into account the trends of co-activation

Examples Methods Patients and Tissue Samples

The present study was organized by the CHEMORES initiative (Chemotherapy resistance consortium), which is an EU funded (FP6) Integrated Project involving 19 academic centres, organizations for cancer research, and research-oriented biotechnology companies in 8 European countries.

Tissue samples from a cohort of 123 patients who underwent complete surgical resection at the Institut Mutualiste Montsouris (Paris, France) between 30 Jan. 2002 and 26 Jun. 2006 were analysed. Clinical characteristics are given in Table 4 below. The median age of patients was 63 years (range 41-85), 34 (28%) were female and 89 (72%) were male. The histopathology of all tumors was reviewed by the same pathologist (JvdO): 50 patients had SCC, 57 AC, 13 LCC and 3 unclassified. Using the new 7th edition TNM staging 56 were stage I, 25 stage II, 28 stage III and 4 stage IV. Adjuvant platinum based chemotherapy was administered to 61 patients. Fifty-nine patients experienced a relapse. Two-year relapse-free survival was 64%, and the median time to recurrence for the cohort was 5.2 years. After a median follow up of 40 months (range 0-92) 36 patients had died and 23 patients were alive with recurrence.

This study was performed using snap-frozen tumor and adjacent normal lung tissue. Samples were handled according to the Tumor Analysis Best Practices Working Group (Nat Rev Genet 2004; 5:229-237). Haematoxylin and eosin stained frozen sections, taken before and after the cutting of slides for analysis, revealed a median cell content of 85% (an inter-quartile range of 65% to 95%). All tissues were banked after written informed patient consent, and the study was approved by the Ethics Committee of Institut Gustave Roussy (IGR). Genomic investigations were performed at IGR, leader of the Genomic work-package of Chemores consortium, in the genomic center core facility certified ISO9001, labelled European reference and training center for Agilent technologies. Analyses were performed at IGR and Karolinska Institute, the leader of integrated analyzes work-package.

TABLE 2 Characteristics of the patients in the study population n = 123 (100%) Age median (range)   63 (40.9-84.6) Males n (%) 89 (72%) Smoking Current 64 (52%) Former 51 (42%) Never 7 (6%) Histology AC 57 (46%) SCC 50 (41%) LCC 13 (11%) Other 3 (3%) Stage 1 56 (50%) 2 25 (22%) 3 28 (25%) 4 4 (4%) Adjuvant Chemo (%) 61 (50%)

Data Availability

The microarray data related to this study have been submitted to the Array Express data repository at the European Bioinformatics Institute (http://www.ebi.ac.uk/arrayexpress/) under the accession numbers E-MTAB-1132 (GE), E-MTAB-1133 (CGH) and E-MTAB-1134 (MIR).

Oligonucleotide aCGH

DNA samples were extracted from tissues using Qiagen QIAamp DNA Mini kit (Qiagen, Hilden, Germany). In each case, the normal tissue sample was used as the reference to its corresponding tumor sample. DNA was restriction digested and controlled by Agilent Bioanalyzer on DNA 7500 chips (Agilent Technologies, Santa Clara, Calif., USA). The fragmented reference and test DNA were labelled with Cy3-dUTP or Cy5-dUTP, respectively, using Agilent Genomic DNA Labelling Kit PLUS. Samples were purified using Microcon YM-30 filters (Millipore, Billerica, Mass.). Hybridization was carried out on Agilent 244K arrays for 24 hours at 65° C. in a rotating oven (Robbins Scientific, Mountain View, Calif.) at 20 rpm, followed by appropriate washing steps. Scanning was performed with an Agilent G2505C DNA Microarray scanner using default parameters. Quantification of Cy5 and Cy3 signals from scans was performed with Feature Extraction v10.5.1.1 (Agilent Technologies) using default parameters.

CGH Data Processing and Analysis

Resulting raw signals and log 2 (ratio) profiles were normalized and centered according to their dye composition (Cy5/Cy3) and local GC content. These profiles were segmented with the Circular Binary Segmentation algorithm (Olshen et al. Biostatistics 2004 October; 5(4):557-72) through its implementation in the DNAcopy package for R v2.8.1 using default parameters. DNA copy number imbalances were detected considering a minimum of 3 consecutive probes and a minimal absolute amplitude threshold that was specific for each profile, accordingly with its internal noise. This specific internal noise was computed as one-fourth of the median of the absolute log 2 (ratio) distances across consecutive probes on the genome. Of the 128 aCGH hybridizations performed, 17 were discarded: 7 due to their clinical annotations, 2 due to anomalies in their normal reference, and 8 due to the bad quality of their profile, resulting in 111 usable profiles. All aCGH coordinates in this study are mapped against the human genome as defined by the UCSC build hg18.

To assess the discovery of the genomic regions with differential anomalies between the AC, LCC and SCC populations, ANOVA tests were performed on the segmented aCGH dataset. To account for multiple testing, p-values were transformed to false discovery rate (FDR) (Benjamini et al. J Royal Statist Soc B 1995; 57:289-300).

Gene Expression and microRNA Microarray Assay

The lysis of 40 to 50 frozen sections of 10 micron-thickness, cut from each NSCLC tissue sample was done using a Polytron homogenizer (Ultraturrax, IMLAB, Lille, France). The RNA extraction was performed with TRIzol® Reagent protocol (Invitrogen, Carlsbad, Calif., USA). Total RNA was quantified and qualified with Nanodrop ND-1000 spectrometer and Bioanalyzer-2100 (Agilent Technologies).

For dual color Cy3 (normal samples) and Cy5 (tumor samples) labelling, Agilent Fluorescent Low Input Linear Amplification kit adapted for small amounts of total RNA (500 ng total RNA per reaction) was used, followed by purification of labelled probes by Qiagen RNeasy Mini kit and by a protocol provided by Agilent. Gene expression profiling was performed with dye-swap, using dual-color 244K Human exon array from Agilent (custom design with the content of the 44K Human genome plus 195000 probes, one for each exon as defined in refGene list of UCSC build hg18 (http://genome.ucsc.edu/)). Hybridization was carried out for 17 hours at 65° C. at 10 rpm, followed by washing steps. Scanned microarray images were analyzed by using Feature Extraction software version 10.5.1.1 (Agilent).

For the microRNA analysis, normal and tumor samples were hybridized on separate arrays. Agilent miRNA Microarray System with miRNA complete labelling and hybridization kit was used for Cy3 labelling. Briefly, isolated total RNAs were dephosphorylated, labelled with pCp-Cy3 and hybridized to Agilent 8×15K arrays for 20 h at 55° C. in a rotating oven (Robbins Scientific) at 20 rpm. Slides were washed and scanned for gene expression using an Agilent G2565C DNA microarray scanner using defaults parameters.

Gene Mutations Analysis

Sequencing was performed at IGR and at the Royal Institute of Technology (Stockholm, Sweden). DNA was extracted with QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). After PCR amplification of target exons, sequencing reactions were carried out using the BigDye® Terminator Cycle Sequencing Kit (Applied Biosystems, Forster City, Calif.). The primer sequences are available on request. Sequencing reactions were run on a 48-capillary 3730 DNA Analyzer®. Sequence analysis and alignment was performed with SeqScape® software (Applied Biosystems). All detected mutations were confirmed in at least one independent PCR reaction. In all 123 samples, full coding sequences of exons including oncogenic mutational hotspots were analyzed corresponding to: TP53 (NM_000546.4) exons 5-8; KRAS (NM_004448.2) exons 2 and 3; EGFR (NM_005228.3) exons 18-21; PIK3CA (NM_006218.2) exons 10 and 21; BRAF (NM_004333.4) exon 15; ERBB2 (NM_004448.2) exons 18, 20-24; KDR (NM_002253.1) exons 2, 26, 27 and 30; and AKT1 (NM_005163.2) exon 4.

Gene-Expression Data Processing and Normalisation

All processing methods used for gene expression analysis were performed on the median signal from Agilent Feature Extraction raw data files using functions and packages collected in the R Bioconductor project (Gentleman et al. Genome Biology, 5: R80) as well as custom written routines.

For gene expression data, dye-swap arrays were first combined (by taking the average of intensities) to obtained only one array per condition. This combination has the result of centering the M values (log 2 ratios) on zero. Then, flagged spots as well as control spot were removed. Normalization was then performed using the normalizeWithinArrays function from R package LIMMA (Smyth G K Statistical Applications in Genetics and Molecular Biology 2004, vol 3: No. 1, article 3).

For miRNA data, control spots were systematically removed, and flagged spots (glsFeatNonUnifOL and glsSaturated columns from raw files) were considered as missing values (“NA”). Array normalization was performed using the least-variant-set method (Suo et al. RNA 2010 December; 16(12): 2293-303).

Differential Expression Analyses of miRNA Expression

To assess differentially-expressed miRNA, the inventors first estimated the fold changes and standard errors between two groups of samples by fitting a linear model for each probe with the ImFit function of LIMMA package in R. Then they applied an empirical Bayes smoothing to the standard errors from the linear model previously computed with eBayes function.

Scoring/Ranking of Activated Interventional Points The Algorithm

The mathematical modelling and scoring system aims to give a score (1 to 10) based on integration of omics data, sequencing, gene expression, miRNA and copy number variations determined as differences between tumor and normal, individually for each patients. SPRING scoring enables identification and ranking of activated pathways, and the overall concept is that such activated pathways should be blocked with combined targeted therapies.

The first mathematical model was established on the basis of a retrospective dataset from 123 patients with NSCLC for whom sequencing, Copy Number Variation, and tumor vs. normal gene expression were available. Using these data, an algorithm that provides a score of activation for each of the simplified pathway for the patient and factors in all of the above-mentioned structural and functional results has been established. The principle of the algorithm is disclosed in FIG. 2.

Scoring is based on an intuitive algorithm that integrates 4 types of genomic investigations of Tumor and Normal biopsies

-   -   1. Mutations: in V.1 the inventors used a very limited set of         sequencing data, including only the genes/mutations used         currently in clinical care of NSCLC: EGFr, kRAS, BRAF, PI3KCA,         and HER2. Additionally they sequenced p53, the most frequent         mutated gene in lung (and all solid tumors).         -   a. When a mutation is detected, the algorithm assign the             maximal score 10 in the corresponding simplified pathway.     -   2. Gene Expression: For each simplified pathway, mRNA steady         state level in Tumor vs. Normal is used to calculate a mean fold         change of the pathway.         -   a. Values of individual Fold Change are trimmed at the             threshold 1.3.         -   b. Values of individual mean fold changes for each             simplified pathway are ranked in the retrospective set of             data of 123 NSCLC, used as a calibrator.         -   c. As shown in 3 examples below, the range of Fold Changes             is different from one to other pathway. In order to compare             them, the inventors generated a relative scoring from 1 to             10 based on the percentile calculation.     -   3. miRNA expression: For each gene, the inventors selected top 5         matched miRNA from TargetScan data base.         -   a. The fold changes T vs. N steady state level for each             miRNA was used to generate a mean fold change.         -   b. Fold change T vs. N for each gene was divided by the mean             Fc T/N of the 5 corresponding miRNAs.         -   c. They generated then a corrected mean Fold change for each             simplified pathway.         -   d. They generated a corrected score 1 to 10 based on             percentiles.     -   4. Copy Number Variation. When amplification is detected, the         inventors multiplied the value of the mRNA expression fold         change for each gene by the value of the fold change         amplification. Then they generate the corrected mean fold change         of pathways and the percentiles score.

TABLE 3 summarises scores obtained for all patients of the 123 NSCLC, for a selection of interventional points patient Histo Her CDK4_6 ANGIO PI3K MET MEK ERK FGF mTOR RAS RAF PARP JAK_STAT PDL1 CTLA4 AGG600716 AC 1 3 5 2 4 9 3 5 5 6 3 8 6 9 9 ANO420520 AC 5 6 7 7 10 2 1 3 2 7 4 5 8 10 9 ARC270517 SCC 9 4 1 1 1 3 1 8 2 3 2 8 2 1 4 AVI260916 AC 2 2 5 7 2 8 9 9 7 10 10 5 8 9 2 AZE450213 AC 8 10 9 4 7 7 5 2 3 2 9 3 9 2 10 BAR331123 SCC 8 7 10 10 6 4 7 9 8 8 8 7 7 7 10 BAS260512 AC 10 1 3 1 3 5 2 1 4 4 5 6 5 5 3 BAS260724 AC 5 10 8 3 9 6 5 2 1 6 5 4 5 10 8 BEM291129 SCC 5 1 1 6 5 4 6 6 2 5 4 1 8 5 7 BEN480707 SCC 1 1 2 4 5 8 4 2 3 9 6 2 7 10 5 BEN410529 LCC 7 3 9 5 5 7 3 6 2 10 10 5 6 8 8 BER520430 AC 7 2 4 2 3 3 4 6 7 7 3 2 1 4 2 BIE410219 SCC 10 9 7 7 5 7 6 9 7 10 4 9 8 3 8 BOU480910 AC 9 3 6 2 5 8 2 7 5 6 4 3 6 3 6 BOU291129 SCC 2 9 1 10 9 3 2 5 7 1 1 10 3 4 1 BOU520111 AC 6 5 5 5 6 2 9 8 7 1 6 5 4 6 10 BRO521127 AC 4 8 8 2 7 9 7 1 2 2 5 6 10 6 10 BRZ470326 AC 10 9 9 8 10 10 5 6 10 2 1 8 7 10 8 CAM520101 Other 10 9 6 8 10 9 6 7 4 2 1 1 10 3 7 SCLC CAP460215 LCC 1 4 1 3 10 2 4 2 5 3 10 9 2 2 4 CHA280524 AC 8 5 2 8 9 4 10 1 3 4 5 3 5 1 4 CHA571008 LCC 8 5 5 1 6 2 6 2 1 3 2 5 3 5 6 CHA470718 LCC 4 6 10 3 9 7 10 6 10 3 7 2 5 7 9 CHE511225 AC 6 9 1 2 8 6 8 3 9 3 9 10 9 6 7 COU420201 AC 2 10 1 10 4 5 10 7 8 6 10 10 1 1 5 CRE420423 SCC 6 10 10 6 8 6 1 10 10 9 5 4 7 9 9 DAM200413 SCC 2 10 9 7 2 10 3 3 6 DAV320407 SCC 1 5 10 2 7 3 5 10 4 2 7 6 2 7 7 DEL330821 AC 7 8 7 10 10 9 4 3 9 10 7 4 10 9 10 DEP351121 SCC 5 9 6 8 6 6 10 8 10 2 6 9 2 4 3 DES580418 AC 10 6 3 7 9 7 8 6 8 5 8 10 10 8 7 DEW440406 AC 5 4 6 4 7 3 4 3 3 6 6 2 2 5 5 DHE321214 Other 9 6 3 6 10 4 1 9 5 9 10 6 6 5 5 ADEC DOM590729 SCC 3 10 3 9 7 4 10 8 5 8 4 10 4 10 5 DUV330713 SCC 6 5 10 4 4 8 9 7 9 2 8 10 6 10 4 ECU520713 AC 3 10 8 1 8 2 7 9 10 8 8 3 3 5 1 EDO300812 SCC 7 5 2 9 8 7 4 3 9 7 5 9 5 4 7 ELA540809 LCC 4 8 4 1 1 3 2 10 5 9 10 4 3 5 2 ELB330728 AC 10 3 6 7 7 5 3 2 1 7 6 10 7 6 9 FER471031 AC 4 2 8 2 4 3 4 3 8 4 6 7 2 7 5 FER461230 SCC 3 5 7 6 5 7 2 6 6 5 5 1 4 3 3 FIL381013 AC 10 10 9 6 7 10 3 1 4 3 10 3 10 10 8 FLA490711 AC 5 5 8 1 2 2 5 5 8 1 1 10 1 3 2 FOR440321 AC 7 6 9 6 10 5 7 4 4 1 8 1 7 4 6 FOR410727 SCC 6 7 4 10 3 10 6 3 7 6 4 6 8 10 6 FRO440806 AC 2 2 3 5 6 9 8 1 3 6 8 2 3 5 7 GAN350811 SCC 10 8 4 10 9 6 5 6 6 1 7 8 1 1 3 GAR410813 SCC 6 7 6 9 6 1 10 5 4 4 1 10 6 8 6 GAR450819 SCC 10 7 3 8 4 4 4 2 4 2 4 10 7 8 8 GEF541216 AC 10 7 8 10 3 9 4 8 10 9 4 4 5 9 10 GEO270114 SCC 3 6 2 5 10 5 10 4 1 10 6 7 8 4 7 GID490224 AC 7 7 10 3 8 10 1 3 6 10 9 5 5 3 4 GIL230901 SCC 3 1 2 6 6 6 3 9 7 7 3 6 6 6 6 GIR220606 AC 9 1 3 4 7 4 10 4 4 8 9 2 2 1 3 GOE191205 AC 10 4 7 4 8 1 5 4 2 7 3 3 4 4 2 GOM450227 SCC 9 4 6 9 7 1 2 10 4 6 3 GRO250108 AC 10 9 7 10 6 8 8 4 8 10 10 8 10 8 9 GRY470526 AC 9 6 4 10 9 2 3 2 1 6 7 1 9 2 7 GUI390806 AC 10 7 3 7 3 6 3 10 6 10 10 1 8 2 4 GUI200304 AC 9 2 3 9 9 10 5 10 8 8 10 2 6 2 6 HAM640729 SCC 3 2 10 5 1 10 10 9 1 9 1 5 8 3 1 HAR331217 SCC 10 6 6 10 3 8 1 6 10 1 2 9 2 3 2 HOU501106 AC 8 3 10 6 8 9 10 8 10 5 9 5 10 4 6 IGL380217 AC 1 7 9 5 4 3 6 10 9 3 8 7 3 4 1 ISA300917 SCC 3 4 2 4 2 1 6 5 5 8 4 6 9 3 4 IVA360731 SCC 1 2 5 7 1 7 7 1 2 8 7 1 9 6 5 JAY440311 AC 7 1 8 4 2 1 2 1 5 9 3 1 4 8 6 JEA320618 LCC 10 1 3 10 9 8 6 8 8 6 10 5 9 10 5 KEI431016 SCC 4 4 9 8 9 8 4 7 10 6 4 2 4 9 9 KON381027 AC 9 8 10 1 1 2 2 1 9 1 4 3 1 2 1 KRA420928 AC 10 1 8 7 9 7 10 8 8 4 8 1 10 4 9 LAM380228 AC 6 7 10 5 4 5 5 4 4 9 7 5 3 3 4 LAN041130 LCC 10 8 1 4 10 9 1 8 9 5 10 10 4 8 10 LAN510426 SCC 10 9 1 9 3 8 3 9 3 9 7 7 10 10 10 LEF320516 SCC 8 5 10 3 8 1 9 8 8 1 2 5 3 5 1 LEF341111 SCC 7 9 8 1 2 3 9 10 10 1 2 9 2 2 3 LEJ501115 SCC 1 2 5 3 5 2 7 1 1 3 2 4 8 7 4 LEL450721 AC 1 10 1 2 10 2 8 5 9 1 1 6 7 2 9 LEM351012 LCC 9 8 4 6 3 2 6 1 10 1 2 10 1 1 1 LEN371015 SCC 3 3 1 3 6 1 10 10 9 6 1 7 5 1 3 LEP560531 AC 8 2 10 8 7 3 1 3 2 5 6 3 1 2 6 LER460716 SCC 2 1 10 5 3 3 2 5 3 9 7 4 6 6 8 MAC460101 AC 7 1 8 1 1 5 8 2 2 4 5 7 7 6 4 MAC381220 SCC 4 4 4 2 7 10 8 5 7 5 9 3 2 7 1 MAR240911 SCC 5 2 5 2 1 6 7 10 5 5 7 4 2 3 4 MAR491126 SCC 7 9 4 3 4 2 10 9 8 7 MAR430726 AC 9 4 8 6 3 5 6 5 3 2 7 7 5 6 7 MAR350507 SCC 7 6 5 10 6 6 9 7 8 1 9 8 9 6 5 MAR470322 LCC 3 5 7 2 5 8 7 5 7 5 5 10 9 9 9 MAT230414 SCC 4 10 2 10 4 5 7 7 10 5 4 1 7 4 8 MER490318 AC 10 2 6 8 8 8 2 3 3 10 6 3 4 9 4 NEG410311 AC 10 8 2 8 8 10 2 2 9 7 10 6 10 5 6 NIN270409 AC 10 8 7 3 10 9 5 4 3 4 10 2 8 7 7 PAN390607 AC 6 1 9 3 2 1 9 4 1 3 1 1 1 1 1 PEC481113 AC 10 2 5 6 4 1 5 4 2 3 9 2 4 2 2 PER401217 Other 1 4 2 1 2 1 7 9 1 4 6 4 8 8 3 ADEC PER510713 AC 2 3 7 4 6 8 1 4 5 7 8 2 6 7 8 PIQ340906 SCC 5 1 9 1 1 7 7 2 6 4 2 4 1 5 2 RAB330621 SCC 6 8 5 10 2 4 6 9 2 8 5 8 2 2 2 RAM530325 AC 9 8 7 3 5 9 1 7 6 4 5 4 3 8 3 REC590707 LCC 4 9 6 8 3 10 9 6 10 3 3 9 1 8 5 REJ471005 SCC 10 6 4 9 5 7 9 9 6 2 2 8 10 6 10 RIT431108 AC 10 10 4 9 9 4 9 6 1 10 8 6 10 10 10 RIT490630 SCC 2 6 7 7 3 9 7 5 4 7 7 9 6 5 9 SAI380426 AC 5 8 10 9 8 4 5 10 7 8 1 1 6 8 3 SAU450710 SCC 3 5 2 2 1 5 9 10 1 8 5 7 1 1 1 SER300810 LCC 2 4 10 1 5 7 9 4 2 5 9 2 5 7 2 SIK471101 AC 8 3 8 5 10 5 8 2 4 10 6 3 5 6 7 SUT470608 SCC 4 3 9 7 4 6 2 5 7 4 3 9 5 7 5 TAI320613 AC 10 5 5 3 2 4 8 1 3 8 1 9 3 7 1 TAR290829 SCC 3 7 3 4 1 1 8 8 1 2 3 8 3 2 3 TAT400901 AC 9 6 10 5 10 3 1 7 6 10 2 5 4 3 6 THU220630 SCC 2 3 7 4 5 4 1 7 5 8 3 6 4 8 3 TIL420228 SCC 10 4 4 6 7 6 8 7 5 4 6 7 9 10 8 UST500306 SCC 1 10 1 10 1 5 4 4 6 3 1 9 4 1 9 VAL271009 SCC 5 3 6 5 2 6 6 8 6 5 9 8 8 9 5 VIL310309 SCC 6 10 9 8 8 1 4 6 9 9 2 8 7 9 10 WIS320823 SCC 2 3 1 8 2 9 3 7 3 9 3 9 10 10 8 YOT471216 AC 2 7 4 9 4 10 3 3 6 7 8 6 9 7 10 ZIT420630 AC 8 7 10 9 6 10 8 10 7 7 8 3 9 9 2

In the next step, the inventors made the selection of all activated interventional points. Scores 8, 9 and 10 were considered designating an important/high activation, whereas scores 6 and 7 were considered designating medium activation. Scores<6 were considered as designating non activated interventional points.

In a preferred embodiment, the frequence of activation of inteventional points (score>5), enabling determination of the most rationale combinations is the following

TABLE 5 Trends of cooactivation of interventional points Ras/ mtor/ CTLA4 PD1L mek mTor pi3k ERK met AurkA cdk4,6 HER Angio FGF PARP RAF IGF DNAREP PI3K ID Histo 61 63 54 59 55 57 51 55 60 68 56 47 47 88 44 56 83 N° 123 patients 50 51 44 48 45 46 41 45 49 55 46 38 38 72 36 46 67 % 100

TABLE 6 Selection of most frequent combinations taking into account trends of coactivation. For each of the first and second drug number of patients (upper case) and % (lower case) are showed. For each of the third drug number of patients out of 123 and % are shown. First drug NB/% Second drug NB/% Third drug Nb % RAS/RAF 88 mTor/PI3K 60 PD1L 34 28 CTLA4 33 27 CDK4,6 32 26 AURKA 29 24 DNARepair 28 23 72 49 ANGIO 27 22 MET 27 22 FGF 26 21 PARP 24 20 IGF 23 19 RAS/RAF 88 MET 40 CTLA4 32 26 mTor/PI3K 27 22 PD1L 22 18 ANGIO 20 16 CDK4,6 21 17 72 33 AURKA 17 14 FGF 17 14 DNARepair 15 12 IGF 13 11 PARP 12 10 RAS/RAF 88 CDK4,6 40 mTor/PI3K 32 26 CTLA4 27 22 AURKA 23 19 MET 21 17 PD1L 20 16 72 33 DNARepair 20 16 ANGIO 17 14 FGF 17 14 PARP 17 14 IGF 12 10 mTor/PI3K 83 RAS/RAF 60 PD1L 34 28 CTLA4 33 27 CDK4,6 32 26 AURKA 29 24 DNARepair 28 23 67 49 MET 27 22 ANGIO 27 22 FGF 26 21 PARP 24 20 IGF 23 19 CDK4,6 63 RAS/RAF 51 mTor/PI3K 34 28 CTLA4 27 22 ANGIO 24 20 IGF 23 19 MET 22 18 51 41 AURKA 22 18 CDK4,6 20 16 PD1L 20 16 FGF 19 15 PARP 16 13 PD1L 63 mTor/PI3K 42 RAS/RAF 34 28 CTLA4 25 20 DNARepair 23 19 CDK4,6 21 17 ANGIO 21 17 51 34 AURKA 20 16 IGF 19 15 FGF 18 15 MET 16 13 PARP 15 12 MEK 54 RAS/RAF 42 CTLA4 29 24 PD1L 28 23 mTor/PI3K 28 23 CDK4,6 19 15 ANGIO 19 15 44 34 IGF 19 15 AURKA 16 13 FGF 16 13 DNARepair 15 12 parp 11 9 CDK4,6 60 mTor/PI3K 48 RAS/RAF 32 26 AURKA 32 26 DNARepair 32 26 CTLA4 29 24 parp 26 21 49 39 FGF 23 19 MET 22 18 PD1L 21 17 ANGIO 20 16 IGF 15 12 MET 51 RAS/RAF 40 CTLA4 32 26 mTor/PI3K 27 22 PD1L 22 18 ANGIO 21 17 MEK 19 15 41 33 AURKA 17 14 FGF 17 14 DNARepair 15 12 IGF 13 11 PARP 12 10 ANGIO 56 RAS/RAF 41 mTor/PI3K 27 22 PD1L 24 20 MET 20 16 MEK 19 15 AURKA 19 15 46 33 IGF 17 14 CDK4,6 16 13 FGF 15 12 DNARepair 14 11 PARP 7 6

TABLE 7 summarizes the most frequent triple combinations First drug NB Second drug NB Third drug Nb % RAS/RAF 88 mTor/PI3K 60 PD1L 34 28 RAS/RAF 88 mTor/PI3K 60 CTLA4 33 27 RAS/RAF 88 mTor/PI3K 60 CDK4,6 32 26 RAS/RAF 88 mTor/PI3K 60 AURKA 29 24 RAS/RAF 88 mTor/PI3K 60 DNARepair 28 23 RAS/RAF 88 mTor/PI3K 60 ANGIO 27 22 RAS/RAF 88 mTor/PI3K 60 MET 27 22 RAS/RAF 88 mTor/PI3K 60 FGF 26 21 RAS/RAF 88 MET 40 CTLA4 32 26 RAS/RAF 88 CDK4,6 40 CTLA4 27 22 CDK4,6 63 RAS/RAF 51 ANGIO 24 20 CDK4,6 60 mTor/PI3K 48 AURKA 32 26 CDK4,6 60 mTor/PI3K 48 DNARepair 32 26 CDK4,6 60 mTor/PI3K 48 CTLA4 29 24 CDK4,6 60 mTor/PI3K 48 PARP 26 21 MEK 54 RAS/RAF 42 CTLA4 29 24 MEK 54 RAS/RAF 42 PD1L 28 23 MEK 54 RAS/RAF 42 mTor/PI3K 28 23

TABLE 8 Summarizes the most frecquent combinations involving and immunomodulator First drug NB Second drug NB Third drug Nb % RAS/RAF 88 mTor/PI3K 60 PD1L 34 28 RAS/RAF 88 MET 40 PD1L 22 18 RAS/RAF 88 CDK4,6 40 PD1L 20 16 PD1L 63 mTor/PI3K 42 DNARepair 23 19 PD1L 63 mTor/PI3K 42 CDK4,6 21 17 PD1L 63 mTor/PI3K 42 ANGIO 21 17 PD1L 63 mTor/PI3K 42 AURKA 20 16 PD1L 63 mTor/PI3K 42 IGF 19 15 PD1L 63 mTor/PI3K 42 FGF 18 15 PD1L 63 mTor/PI3K 42 MET 16 13 ANGIO 56 RAS/RAF 41 PD1L 24 20 RAS/RAF 88 mTor/PI3K 60 CTLA4 33 27 RAS/RAF 88 MET 40 CTLA4 32 26 RAS/RAF 88 CDK4,6 40 CTLA4 27 22 CDK4,6 63 RAS/RAF 51 CTLA4 27 22 PD1L 63 mTor/PI3K 42 CTLA4 25 20 MEK 54 RAS/RAF 42 CTLA4 29 24 CDK4,6 60 mTor/PI3K 48 CTLA4 29 24 MET 51 RAS/RAF 40 CTLA4 32 26

TABLE 9 Detailed List of genes Pathway Symbol GeneID Name Refseq HER EGF 1950 epidermal growth factor NM_001963 TGFA 7039 transforming growth factor, alpha NM_003236 AREG 374 amphiregulin NM_001657 EREG 2069 epiregulin NM_001432 HBEGF 1839 heparin-binding EGF-like growth factor NM_001945 BTC 685 betacellulin NM_001729 NRG1 3084 neuregulin 1 AF176921; NM_004495 NRG2 9542 neuregulin 2 ENST00000544729; NM_013982 NRG4 145957 neuregulin 4 NM_138573 EGFR 1956 epidermal growth factor receptor NM_201283; NM_201282; NM_005228 ERBB2 2064 v-erb-b2 avian erythroblastic leukemia viral oncogene NM_001005862; homolog 2 AB025286 ERBB3 2065 v-erb-b2 avian erythroblastic leukemia viral oncogene NM_001982; homolog 3 NM_001005915 ERBB4 2066 v-erb-b2 avian erythroblastic leukemia viral oncogene NM_005235 homolog 4 CDK4, 6 CDK4 1019 cyclin-dependent kinase 4 NM_000075 CDK6 1021 cyclin-dependent kinase 6 NM_001259 CCND1 595 cyclin D1 NM_053056 CCND2 894 cyclin D2 NM_001759 CCND3 896 cyclin D3 NM_001760 CDKN2A, 1029 cyclin-dependent kinase inhibitor 2A NM_058197; NM_000077 CDKN2B 1030 cyclin-dependent kinase inhibitor 2B NM_004936 CCNE1 898 cyclin E1 NM_001238 CCNE2 9134 cyclin E2 NM_057749 RB1 5925 retinoblastoma 1 NM_000321 PLK/AURK/ PLK1 5347 polo-like kinase 1 NM_005030 Kinesins AURKA 6790 aurora kinase A NM_198433 BORA 79866 bora, aurora kinase A activator NM_024808 ILK 3611 integrin-linked kinase NM_001014795 KIF11 3832 kinesin family member 11 NM_004523 ANGIOGENESIS VEGFA 7422 vascular endothelial growth factor A NM_001025370; NM_001025366 VEGFB 7423 vascular endothelial growth factor B NM_003377 VEGFC 7424 vascular endothelial growth factor C NM_005429 VEGFD 2277 c-fos induced growth factor (vascular endothelial growth NM_004469 factor D) FLT1 2321 fms-related tyrosine kinase 1 NM_001160031; NM_002019 KDR 3791 kinase insert domain receptor (a type III receptor tyrosine NM_002253 kinase) FLT4 2324 fms-related tyrosine kinase 4 ENST00000376868; NM_002020 PDGFA 5154 platelet-derived growth factor alpha polypeptide NM_002607; NM_033023 PDGFB 5155 platelet-derived growth factor beta polypeptide NM_002608 PDGFRA 5156 platelet-derived growth factor receptor, alpha polypeptide NM_006206 PDGFRB 5159 platelet-derived growth factor receptor, beta polypeptide NM_002609 Kit 3815 v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene NM_000222; homolog NM_001093772 ANGIOPOIETINS THBS1 7057 thrombospondin 1 NM_003246 TGFB1 7040 transforming growth factor, beta 1 NM_000660 ANGPT1 284 angiopoietin 1 NM_001146 ANGPT2 285 angiopoietin 2 NM_001147 ANGPTL1 9068 angiopoietin-like 1 NM_004673 ANGPT4 51378 angiopoietin 4 NM_015985 TIE1 7075 tyrosine kinase with immunoglobulin-like and EGF-like NM_005424 domains 1 TEK 7010 TEK tyrosine kinase, endothelial NM_000459 IMMUNO- CD274 or 29126 CD274 molecule NM_014143 Modulator PDL1 programmed cell death ligand 1 PDCD1LG2 80380 programmed cell death 1 ligand 2 NM_025239 PDCD1 5133 programmed cell death 1 NM_005018 CTLA4 1493 cytotoxic T-lymphocyte-associated protein 4 NM_005214 LAG3 3902 lymphocyte-activation gene 3 NM_002286 PI3K PIK3CA 5290 phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic NM_006218 subunit alpha PIK3CB 5291 phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic NM_006219 subunit beta PIK3CD 5293 phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic, NM_005026 catalytic subunit delta PIK3CG 5294 phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic NM_002649 subunit gamma PIK3C2B 5287 phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic NM_002646; subunit type 2 beta ENST00000367184 PRKCB 5579 protein kinase C, beta NM_002738 PRKCA 5578 protein kinase C, alpha NM_002737 PIK3R1 5295 phosphoinositide-3-kinase, regulatory subunit 1 (alpha) NM_181523 PIK3R2 5296 phosphoinositide-3-kinase, regulatory subunit 2 (beta) NM_005027 PIK3R3 8503 phosphoinositide-3-kinase, regulatory subunit 3 (gamma) NM_003629 MET HGF 3082 hepatocyte growth factor (hepapoietin A; scatter factor) NM_001010934; NM_001010931 MET 4233 met proto-oncogene NM_000245 AXL 558 AXL receptor tyrosine kinase NM_021913 MST1R 4486 macrophage stimulating 1 receptor (c-met-related tyrosine NM_002447 kinase) MEK MAP2K1 5604 mitogen-activated protein kinase kinase 1, E3 ubiquitin NM_002755 protein ligase MAP2K2 5605 mitogen-activated protein kinase kinase 2 NM_030662 MAP2K3 5606 mitogen-activated protein kinase kinase 3 NM_145109; ENST00000534743 MAP2K4 6416 mitogen-activated protein kinase kinase 4 NM_003010 MAP3K1 4214 mitogen-activated protein kinase kinase kinase 1 NM_005921 MAP3K2 10746 mitogen-activated protein kinase kinase kinase 2 NM_006609 MAP3K3 4215 mitogen-activated protein kinase kinase kinase 3 NM_203351 MAP3K4 4216 mitogen-activated protein kinase kinase kinase 4 NM_005922; NM_006724 ERK MAPK3 5595 mitogen-activated protein kinase 3 NM_002746 MAPK1 5594 mitogen-activated protein kinase 1 NM_138957 KSR1 8844 kinase suppressor of ras 1 NM_014238 MAPK11 5600 mitogen-activated protein kinase 11 NM_002751 ANTI- BCL2 596 B-cell CLL/lymphoma 2 NM_000633; APOPTOSIS NM_000657 BCL2L1 598 BCL2-like 1 NM_138578 BIRC5 332 baculoviral IAP repeat containing 5 NM_001012271 XIAP 331 X-linked inhibitor of apoptosis NM_001167 BAK1 578 BCL2-antagonist/killer 1 NM_001188 FGF FGF1 2246 fibroblast growth factor 1 (acidic) NM_000800; NR_026696 FGF2 2247 fibroblast growth factor 2 (basic) NM_002006 FGF3 2248 fibroblast growth factor 3 NM_005247 FGF4 2249 fibroblast growth factor 4 NM_002007 FGF5 2250 fibroblast growth factor 5 NM_004464; NM_033143 FGF6 2251 fibroblast growth factor 6 NM_020996 FGF7 2252 fibroblast growth factor 7 NM_002009 FGF8 2253 fibroblast growth factor 8 (androgen-induced) NM_033163 FGF9 2254 fibroblast growth factor 9 NM_002010 FGF10 2255 fibroblast growth factor 10 NM_004465 FGF11 2256 fibroblast growth factor 11 NM_004112 FGF12 2257 fibroblast growth factor 12 NM_004113 FGF13 2258 fibroblast growth factor 13 NM_004114 FGF14 2259 fibroblast growth factor 14 NM_175929 FGFR1 2260 fibroblast growth factor receptor 1 ENST00000496296; NM_023110; NM_001174066 FGFR2 2263 fibroblast growth factor receptor 2 ENST00000359354; NM_022970 FGFR3 2261 fibroblast growth factor receptor 3 NM_000142 FGFR4 2264 fibroblast growth factor receptor 4 NM_213647 mTOR- mTor 2475 mechanistic target of rapamycin (serine/threonine kinase) NM_004958 AKT- AKT1 207 v-akt murine thymoma viral oncogene homolog 1 NM_005163 PTEN- AKT2 208 v-akt murine thymoma viral oncogene homolog 2 NM_001626 PTEN 5728 phosphatase and tensin homolog NM_000314 Modulators MTKPT TSC1 7248 tuberous sclerosis 1 NM_000368; ENST00000403810 TSC2 7249 tuberous sclerosis 2 NM_000548; NM_001077183 STK11 6794 serine/threonine kinase 11 NM_000455 PIM1 5292 pim-1 oncogene NM_002648 PIM2 11040 pim-2 oncogene NM_006875 PIM3 415116 pim-3 oncogene NM_001001852 RAS KRAS 3845 Kirsten rat sarcoma viral oncogene homolog NM_033360; NM_004985 NRAS 4893 neuroblastoma RAS viral (v-ras) oncogene homolog NM_002524 HRAS 3265 Harvey rat sarcoma viral oncogene homolog NM_005343 RAF RAF1 5894 v-raf-1 murine leukemia viral oncogene homolog 1 NM_002880 BRAF 673 v-raf murine sarcoma viral oncogene homolog B NM_004333 TELOMERASE TERT 7015 telomerase reverse transcriptase NM_198253 TERC 7012 telomerase RNA component NR_001566 TEP1 7011 telomerase-associated protein 1 NM_007110 HSP90AA1 3320 heat shock protein 90 kDa alpha, class A member 1 NM_001017963; NM_005348 DKC1 1736 dyskeratosis congenita 1, dyskerin NM_001363 PTGES3 10728 prostaglandin E synthase 3 NM_006601 IGF & Warburg IGF1 3479 insulin-like growth factor 1 (somatomedin C) NM_000618 IGF2 3481 insulin-like growth factor 2 (somatomedin A) NM_000612 IGF1R 3480 insulin-like growth factor 1 receptor NM_000875 IGF2R 3482 insulin-like growth factor 2 receptor NM_000876 INSR 3643 insulin receptor NM_000208 IRS1 3667 insulin receptor substrate 1 NM_005544 PKM 5315 pyruvate kinase, muscle NM_001206796.1 WNT CDH1 999 cadherin 1, type 1, E-cadherin (epithelial) NM_004360 CTNNA1 1495 catenin (cadherin-associated protein), alpha 1, 102 kDa NM_001903 CTNNB1 1499 catenin (cadherin-associated protein), beta 1, 88 kDa NM_001904; NM_001098210 WNT1 7471 wingless-type MMTV integration site family, member 1 NM_005430 FZD1 8321 frizzled class receptor 1 NM_003505 WNT5A 7474 wingless-type MMTV integration site family, member 5A NM_003392 WNT5B 81029 wingless-type MMTV integration site family, member 5B NM_030775 FZD5 7855 frizzled class receptor 5 NM_003468 WIF1 11197 WNT inhibitory factor 1 NM_007191 DKK1 22943 dickkopf WNT signaling pathway inhibitor 1 NM_012242 PARP PARP1 142 poly (ADP-ribose) polymerase 1 NM_001618; ENST00000366790 BRCA1 672 breast cancer 1, early onset NM_007300 XRCC1 7515 X-ray repair complementing defective repair in Chinese NM_006297 hamster cells 1 RAD54L 8438 RAD54-like (S. cerevisiae) NM_003579 RAD54B 25788 RAD54 homolog B (S. cerevisiae) NM_012415; NM_001205262 ATM 472 ataxia telangiectasia mutated NM_000051; ENST00000389511 ATR 545 ataxia telangiectasia and Rad3 related NM_001184 CHEK1 1111 checkpoint kinase 1 NM_001114121 CHEK2 11200 checkpoint kinase 2 NM_145862; NM_001005735 WEE1 7465 WEE1 G2 checkpoint kinase NM_003390 HDAC HDAC1 3065 histone deacetylase 1 NM_004964 HDAC2 3066 histone deacetylase 2 NM_001527 HDAC3 8841 histone deacetylase 3 NM_003883 HDAC4 9759 histone deacetylase 4 NM_006037 HDAC5 10014 histone deacetylase 5 NM_001015053 JAK-STAT JAK1 3716 Janus kinase 1 NM_002227 JAK2 3717 Janus kinase 2 NM_004972 STAT1 6772 signal transducer and activator of transcription 1, 91 kDa NM_139266 STAT2 6773 signal transducer and activator of transcription 2, 113 kDa NM_005419 STAT3 6774 signal transducer and activator of transcription 3 (acute- NM_213662 phase response factor) SOCS1 8651 suppressor of cytokine signaling 1 NM_003745 HEDGEHOG SHH 6469 sonic hedgehog NM_000193 PTCH1 5727 patched 1 NM_001083602; ENST00000375290 SMO 6608 smoothened, frizzled class receptor NM_005631 STK36 27148 serine/threonine kinase 36 NM_015690 PRKACA 5566 protein kinase, cAMP-dependent, catalytic, alpha NM_002730 SUFU 51684 suppressor of fused homolog (Drosophila) NM_016169; NM_001178133 GLI1 2735 GLI family zinc finger 1 NM_005269 DNA REPAIR ERCC1 2067 excision repair cross-complementation group 1 NM_202001 RAD52 5893 RAD52 homolog (S. cerevisiae) NM_134424; ENST00000545967 XRCC4 7518 X-ray repair complementing defective repair in Chinese NM_022550 hamster cells 4 RAD51 5888 RAD51 recombinase NM_002875 BRCA1 672 breast cancer 1, early onset NM_007300 NEDD8 4738 neural precursor cell expressed, developmentally down- NM_006156 regulated 8 NAE1 8883 NEDD8 activating enzyme E1 subunit 1 NM_001018159 NOTCH NOTCH1 4851 notch 1 NM_017617 Adam17 6868 ADAM metallopeptidase domain 17 NM_003183 PSEN1 5663 presenilin 1 NM_000021; ENST00000394157 NCSTN 23385 nicastrin NM_015331 JAG1 182 jagged 1 NM_000214 SRRT 51593 serrate RNA effector molecule homolog (Arabidopsis) NM_001128853; NM_015908; NM_001128854 APH1A 51107 APH1A gamma secretase subunit NM_016022; NM_001077628 Others ROS1 6098 c-ros oncogene 1, receptor tyrosine kinase ENST00000403284; NM_002944 ALK 238 anaplastic lymphoma receptor tyrosine kinase NM_004304 RET 5979 ret proto-oncogene NM_020630; NM_020975 UBA1 7317 ubiquitin-like modifier activating enzyme 1 NM_003334

TABLE 10 List of genes mutations BRAF Nucleotide Protein c.1799 T > W p.Val600Glu V600E c.1798 G > R p.Val600Lys V600K c.1799 T > W c.1799 T > W c.1800G > R p.Val600Glu V600E c.1780 G > R p.Asp594Asn D594N EGFR Effect on EGFR Nucleotide Protein inhibitors c.2156G > C p.Gly719Ala G719A Sensibility c.2155 G > K p.Gly719Cys G719C Sensibility c.2117 T > Y p.Ile706Thr I706T Sensibility c.2125 G > R p.Glu709Lys E709K Sensibility c.2126 A > M p.Glu709Ala E709A Sensibility c.2174 C > Y p.Thr725Met T725M Sensibility c.2165 C > M p.Ala722Glu A722E Sensibility c.2235_2249 del p.Glu746_Ala750del Deletion E746- Sensibility A750 c.2236_2250 del p.Glu746_Ala750del Deletion E746- Sensibility A750 c.2240_2254del p.Leu747_Thr751del Deletion L747- Sensibility T751 c.2240_2257 del p.Leu747_Pro753delinsSer Deletion L747- Sensibility P753 Insertion S c.2237_2251del p.Glu746_Thr751delinsAla Deletion E746- Sensibility T751 Insertion A c.2239_2248delinsC p.Leu747_Ala750delinsPro Deletion L747- Sensibility A750 Insertion P c.2239_2251delinsC p.Leu747_Thr751delinsPro Deletion L747- Sensibility T751 Insertion P c.2237_2255 delinsT p.Glu746_Ser752delinsVal Deletion E746- Sensibility S752 Insertion V c.2214_2231dup p.Ile740_Lys745dup Duplication I740- Sensibility K745 c.2254_2277 del p.Ser752_Ile759del Deletion S752- Sensibility I759 c.2219_2236dup p.Lys745_Glu746insValProValAlaIleLys K745-E746 Sensibility Insertion VPVAIK c.2277 C > S p.Ile759Met I759M Sensibility c.2239_2256delinsCAA p.Leu747_Ser752delinsGln Deletion L747- Sensibility S752 Insertion Q c.2369C > Y p.Thr790Met T790M Resistance c.2317_2318insACC p.His773dup Duplication H773 Resistance c.2317_2318ins12 p.Pro772_His773insLeuGlyAsnPro P772-H773 Resistance insertion LGNP c.2315_2326dup p.Pro772_Cys775dup Duplication P772- Resistance C775 c.2300_2308 dup p.Ala767_Val769dup Duplication A767- Resistance V769 c.2303_2311 dup p.Ser768_Asp770dup Duplication S768- Resistance D770 c.2303_2311dup p.Ser768_Asp770dup Duplication S768- Resistance D770 c.2335G > T p.Gly779Cys G779C Resistance c.2573 T > K p.Leu858Arg L858R Sensibility c.2582 T > W p.Leu861Gln L861Q Sensibility Nucleotide Protein KRAS-NRAS c.34 G > K p.Gly12Cys G12C c.35 G > R p.Gly12Asp G12D c.35 G > K p.Gly12Val G12V c.35 G > S p.Gly12Ala G12A c.34 G > R p.Gly12Ser G12S c.34 G > S p.Gly12Arg G12R c.38 G > R p.Gly13Asp G13D c.37 G > K p.Gly13Cys G13C c.182 A > W p.Gln61Leu Q61L c.182 A > R p.Gln61Arg Q61R c.183 A > M p.Gln61His Q61H c.176 C > S p.Ala59Gly A59G c.175 G > R p.Ala59Thr A59T c.176 C > M p.Ala59Glu A59E ERBB2 c.2313_2324dup p.Tyr772_Ala775dup Duplication Y772-A775 c.2318_2319insGATGGCATACGT p.Tyr772_Ala775dup Duplication Y772-A775 c.2326_2327insTGT p.Gly776delinsValCys Deletion G776 Insertion VC c.2331_2339dup p.Gly778_Pro780dup Duplication G778-P780 PIK3CA c.1624 G > R p.Glu542Lys E542K c.1633 G > R p.Glu545Lys E545K c.3140A > R p.His1047Arg H1047R c.3140A > W p.His1047Leu H1047L c.2959 G > R p.Ala987Thr A987T c.3052G > A p.Asp1018Asn D1018N c.3080 C > Y p.Ala1027Val A1027V c.3131A > R p.Asn1044Ser N1044S

TABLE 11 List of miRNA Pathway Symbol GeneID miRNAs HER EGF 1950 hsa-miR-4673; hsa-miR-485-5p; hsa-miR-647; hsa-miR-4742-5p; hsa-miR-4797-5p TGFA 7039 hsa-miR-3147; hsa-miR-1178; hsa-miR-626; hsa-miR-148a; hsa-miR-1182 AREG 374 hsa-miR-517a; hsa-miR-34c-5p; hsa-miR-4724-3p; hsa-miR-556-5p; hsa-miR- 517b EREG 2069 hsa-miR-4713-5p; hsa-miR-4645-5p; hsa-miR-130a; hsa-miR-3661; hsa-miR-192 HBEGF 1839 hsa-miR-4736; hsa-miR-1207-5p; hsa-miR-4710; hsa-miR-3160-5p; hsa-miR-1271 BTC 685 hsa-miR-4715-3p; hsa-miR-1200; hsa-miR-4661-5p; hsa-miR-934; hsa-miR-488 NRG1 3084 hsa-miR-4632; hsa-miR-1203; hsa-miR-552; hsa-miR-4736; hsa-miR-183 NRG2 9542 hsa-miR-3196; hsa-miR-3934; hsa-miR-4746-5p; hsa-miR-296-5p; hsa-miR-4665-5p NRG4 145957 hsa-miR-608; hsa-miR-1301; hsa-miR-4704-3p; hsa-miR-516b; hsa-miR-3681; EGFR 1956 hsa-miR-4417; hsa-miR-608; hsa-miR-885-3p; hsa-miR-4474-3p; hsa-miR-7; ERBB2 2064 hsa-miR-331-3p; hsa-miR-4650-5p; hsa-miR-1972; hsa-miR-4533; hsa-miR-1296; ERBB3 2065 hsa-miR-3199; hsa-miR-4505; hsa-miR-1287; hsa-miR-3153; hsa-miR-4290; ERBB4 2066 hsa-miR-4469; hsa-miR-193a-3p; hsa-miR-642a; hsa-miR-3907; hsa-miR-3187-3p; CDK4,6 CDK4 1019 hsa-miR-4747-5p; hsa-miR-198; hsa-miR-4728-5p; hsa-miR-765; hsa-miR-4280; CDK6 1021 hsa-miR-3680; hsa-miR-3158-3p; hsa-miR-621; hsa-miR-644; hsa-miR-4252; CCND1 595 hsa-miR-4707-3p; hsa-miR-3170; hsa-miR-1193; hsa-miR-4740-3p; hsa-miR-4632; CCND2 894 hsa-miR-1468; hsa-miR-103b; hsa-miR-1205; hsa-miR-3065-3p; hsa-miR-4718; CCND3 896 hsa-miR-4701-5p; hsa-miR-4739; hsa-miR-138; hsa-miR-4749-5p; hsa-miR-3154; CDKN2A, 1029 hsa-miR-663b; hsa-miR-675; hsa-miR-663; hsa-miR-1291; hsa-miR-621; CDKN2B 1030 hsa-miR-4308; hsa-miR-718; hsa-miR-1914; hsa-miR-451; hsa-miR-346; CCNE1 898 hsa-miR-16; hsa-miR-874; hsa-miR-146b-3p; hsa-miR-4524; hsa-miR-3190; CCNE2 9134 hsa-miR-449a; hsa-miR-370; hsa-miR-4460; hsa-miR-30b; hsa-miR-485-5p; RB1 5925 hsa-miR-4703-5p; hsa-miR-4801; hsa-miR-4432; hsa-miR-7; hsa-miR-525-5p;

/ PLK1 5347 hsa-miR-296-5p; hsa-miR-4660; hsa-miR-3665; hsa-miR-3166; hsa-miR-4778-5p; AURK/ AURKA 6790 hsa-miR-3941; hsa-miR-4655-5p; hsa-miR-4756-5p; hsa-miR-3616-3p; hsa-miR- Kine 4757-5p;

BORA 79866 hsa-miR-532-3p; hsa-miR-3162-3p; hsa-miR-4713-5p; hsa-miR-4758-3p; hsa-miR- 3189-5p; ILK 3611 hsa-miR-1908; hsa-miR-4505; hsa-miR-744; hsa-miR-4425; hsa-miR-3150a-3p; KIF11 3832 ANGIOGENESIS VEGFA 7422 hsa-miR-3668; hsa-miR-939; hsa-miR-29a; hsa-miR-339-5p; hsa-miR-16; VEGFB 7423 hsa-miR-2467-3p; hsa-miR-4649-3p; hsa-miR-4687-3p; hsa-miR-193a-5p; hsa-miR- 1275; VEGFC 7424 hsa-miR-711; hsa-miR-3688-5p; hsa-miR-4687-3p; hsa-miR-128; hsa-miR-4318; VEGFD 2277 hsa-miR-320e; hsa-miR-135a; hsa-miR-7; hsa-miR-1184; hsa-miR-513b; FLT1 2321 hsa-miR-148a; hsa-miR-5095; hsa-miR-335; hsa-miR-615-3p; hsa-miR-149; KDR 3791 hsa-miR-4435; hsa-miR-665; hsa-miR-370; hsa-miR-136; hsa-miR-138; FLT4 2324 hsa-miR-4707-3p; hsa-miR-2861; hsa-miR-4728-5p; hsa-miR-2467-3p; hsa-miR- 4783-5p; PDGFA 5154 hsa-miR-4690-5p; hsa-miR-3917; hsa-miR-4706; hsa-miR-4768-5p; hsa-miR-412; PDGFB 5155 hsa-miR-3202; hsa-miR-1909; hsa-miR-3689d; hsa-miR-4271; hsa-miR-625; PDGFRA 5156 hsa-miR-3691-3p; hsa-miR-4471; hsa-miR-34a; hsa-miR-663b; hsa-miR-3117-3p; PDGFRB 5159 hsa-miR-1915; hsa-miR-4292; hsa-miR-4731-5p; hsa-miR-637; hsa-miR-486-3p; Kit 3815 hsa-miR-4254; hsa-miR-671-5p; hsa-miR-1193; hsa-miR-222; hsa-miR-4485; ANGIOPOIETINS THBS1 7057 hsa-miR-3074-5p; hsa-miR-4786-3p; hsa-miR-3177-5p; hsa-miR-634; hsa-miR-4443; TGFB1 7040 hsa-miR-3196; hsa-miR-663; hsa-miR-296-5p; hsa-miR-3943; hsa-miR-3183; ANGPT1 284 hsa-miR-153; hsa-miR-4643; hsa-miR-4755-5p; hsa-miR-4789-3p; hsa-miR-3682-3p; ANGPT2 285 hsa-miR-135a; hsa-miR-1182; hsa-miR-513c; hsa-miR-597; hsa-miR-4251; ANGPTL1 9068 hsa-miR-3688-5p; hsa-miR-586; hsa-miR-4480; hsa-miR-544; hsa-miR-194; ANGPT4 51378 hsa-miR-296-5p; hsa-miR-4690-3p; hsa-miR-422a; hsa-miR-431; hsa-miR-665; TIE1 7075 hsa-miR-3151; hsa-miR-4447; hsa-miR-4723-5p; hsa-miR-486-3p; hsa-miR-4287; TEK 7010 hsa-miR-4713-5p; hsa-miR-300; hsa-miR-4690-3p; hsa-miR-150; hsa-miR-148a; IMMUNO- CD274 or 29126 hsa-miR-4443; hsa-miR-3117-3p; hsa-miR-138; hsa-miR-339-5p; hsa-miR-1273; Modulator PDL1 PDCD1LG2 80380 hsa-miR-20a; hsa-miR-548an; hsa-miR-4661-5p; hsa-miR-3133; hsa-miR-3910; PDCD1 5133 hsa-miR-4290; hsa-miR-1291; hsa-miR-4763-5p; hsa-miR-2861; hsa-miR-661; CTLA4 1493 hsa-miR-324-5p; hsa-miR-502-5p; hsa-miR-4254; hsa-miR-3121-5p; hsa-miR-1587; LAG3 3902 hsa-miR-4515; hsa-miR-1269; hsa-miR-4529-3p; hsa-miR-4270; hsa-miR-628-5p; PI3K PIK3CA 5290 hsa-miR-4450; hsa-miR-4529-3p; hsa-miR-302d; hsa-miR-3910; hsa-miR-490-5p; PIK3CB 5291 PIK3CD 5293 hsa-miR-4537; hsa-miR-2355-5p; hsa-miR-523; hsa-miR-7; hsa-miR-484; PIK3CG 5294 hsa-miR-370; hsa-miR-3135b; hsa-miR-1976; hsa-miR-1276; hsa-miR-3672; PIK3C2B 5287 hsa-miR-361-3p; hsa-miR-4728-5p; hsa-miR-4740-3p; hsa-miR-3612; hsa-miR-4314; PRKCB 5579 hsa-miR-4691-5p; hsa-miR-448; hsa-miR-7; hsa-miR-668; hsa-miR-27a; PRKCA 5578 hsa-miR-4757-5p; hsa-miR-4685-5p; hsa-miR-4706; hsa-miR-1275; hsa-miR-4525; PIK3R1 5295 hsa-miR-4789-3p; hsa-miR-4789-5p; hsa-miR-4646-3p; hsa-miR-1184; hsa-miR- 4660; PIK3R2 5296 hsa-miR-4723-5p; hsa-miR-3180; hsa-miR-4447; hsa-miR-3960; hsa-miR-3151; PIK3R3 8503 hsa-miR-4725-3p; hsa-miR-4435; hsa-miR-4715-5p; hsa-miR-2115; hsa-miR-4313; MET HGF 3082 hsa-miR-4520a-3p; hsa-miR-764; hsa-miR-4716-3p; hsa-miR-1288; hsa-miR-4710; MET 4233 hsa-miR-3074-5p; hsa-miR-2682; hsa-miR-34c-5p; hsa-miR-182; hsa-miR-1269b; AXL 558 hsa-miR-3142; hsa-miR-4728-5p; hsa-miR-924; hsa-miR-3689c; hsa-miR-432; MST1R 4486 hsa-miR-296-5p; hsa-miR-218; hsa-miR-1286; hsa-miR-3126-5p; hsa-miR-4284; MEK MAP2K1 5604 hsa-miR-4323; hsa-miR-4423-3p; hsa-miR-758; hsa-miR-34a; hsa-miR-15b; MAP2K2 5605 hsa-miR-1181; hsa-miR-1207-3p; hsa-miR-744; hsa-miR-663; hsa-miR-4786-5p; MAP2K3 5606 hsa-miR-4313; hsa-miR-3151; hsa-miR-4283; hsa-miR-4540; hsa-miR-4270; MAP2K4 6416 hsa-miR-4663; hsa-miR-25; hsa-miR-3065-3p; hsa-miR-4649-5p; hsa-miR-627; MAP3K1 4214 hsa-miR-4286; hsa-miR-1225-3p; hsa-miR-4703-3p; hsa-miR-544; hsa-miR-887; MAP3K2 10746 hsa-miR-519d; hsa-miR-651; hsa-miR-587; hsa-miR-34c-3p; hsa-miR-2909; MAP3K3 4215 hsa-miR-661; hsa-miR-1225-3p; hsa-miR-544b; hsa-miR-3922-3p; hsa-miR-4505; MAP3K4 4216 hsa-miR-1204; hsa-miR-3129-5p; hsa-miR-5047; hsa-miR-3691-3p; hsa-miR-3064- 3p; ERK MAPK3 5595 hsa-miR-4270; hsa-miR-486-3p; hsa-miR-483-5p; hsa-miR-608; hsa-miR-1291; MAPK1 5594 hsa-miR-4667-5p; hsa-miR-4459; hsa-miR-4271; hsa-miR-4799-5p; hsa-miR-2110; KSR1 8844 hsa-miR-331-3p; hsa-miR-4440; hsa-miR-4291; hsa-miR-4660; hsa-miR-876-3p; MAPK11 5600 hsa-miR-4640-3p; hsa-miR-296-5p; hsa-miR-4292; hsa-miR-4532; hsa-miR-4685-5p; ANTI- BCL2 596 hsa-miR-448; hsa-miR-4691-3p; hsa-miR-3199; hsa-miR-3943; hsa-miR-342-3p; APOPTOSIS BCL2L1 598 hsa-miR-4447; hsa-miR-608; hsa-miR-4728-5p; hsa-miR-4649-3p; hsa-miR-4700-5p; BIRC5 332 hsa-miR-542-3p; hsa-miR-3940-3p; hsa-miR-4660; hsa-miR-1225-3p; hsa-miR-1273; XIAP 331 hsa-miR-377; hsa-miR-3150a-3p; hsa-miR-3175; hsa-miR-5095; hsa-miR-3664-5p; BAK1 578 hsa-miR-4419a; hsa-miR-125b; hsa-miR-4667-5p; hsa-miR-1909; hsa-miR-4739; FGF FGF1 2246 hsa-miR-4297; hsa-miR-3155; hsa-miR-1909; hsa-miR-566; hsa-miR-2355-5p; FGF2 2247 hsa-miR-195; hsa-miR-4524; hsa-miR-503; hsa-miR-646; hsa-miR-3607-5p; FGF3 2248 hsa-miR-3173-5p; hsa-miR-4487; hsa-miR-760; hsa-miR-4722-3p; hsa-miR-4758-3p; FGF4 2249 hsa-miR-4671-5p; hsa-miR-3679-3p; hsa-miR-4290; hsa-miR-361-3p; hsa-miR-767- 5p; FGF5 2250 hsa-miR-4435; hsa-miR-4655-5p; hsa-miR-4288; hsa-miR-4463; hsa-miR-4704-3p; FGF6 2251 hsa-miR-4677-3p; hsa-miR-548q; hsa-miR-138; hsa-miR-639; hsa-miR-1322; FGF7 2252 hsa-miR-4762-5p; hsa-miR-486-5p; hsa-miR-195; hsa-miR-3920; hsa-miR-1253; FGF8 2253 hsa-miR-3120-3p; hsa-miR-545; hsa-miR-491-5p; hsa-miR-361-3p; hsa-miR-4720- 5p; FGF9 2254 hsa-miR-1273c; hsa-miR-140-5p; hsa-miR-423-3p; hsa-miR-3157-5p; hsa-miR-3683; FGF10 2255 FGF11 2256 hsa-miR-4667-3p; hsa-miR-4469; hsa-miR-3192; hsa-miR-3661; hsa-miR-3649; FGF12 2257 hsa-miR-4747-5p; hsa-miR-3202; hsa-miR-4533; hsa-miR-4633-3p; hsa-miR-197; FGF13 2258 hsa-miR-1262; hsa-miR-3675-5p; hsa-miR-1185; hsa-miR-512-3p; hsa-miR-4421; FGF14 2259 hsa-miR-4663; hsa-miR-188-3p; hsa-miR-4299; hsa-miR-4690-5p; hsa-miR-4691-3p; FGFR1 2260 hsa-miR-4530; hsa-miR-4728-5p; hsa-miR-515-3p; hsa-miR-1208; hsa-miR-4667-5p; FGFR2 2263 hsa-miR-515-5p; hsa-miR-3177-3p; hsa-miR-423-3p; hsa-miR-4789-3p; hsa-miR- 3675-5p; FGFR3 2261 hsa-miR-296-5p; hsa-miR-4793-3p; hsa-miR-4746-3p; hsa-miR-3918; hsa-miR-1291; FGFR4 2264 hsa-miR-3177-3p; hsa-miR-4726-5p; hsa-miR-1225-3p; hsa-miR-378g; hsa-miR-564; mTOR -AKT- mTor 2475 hsa-miR-767-3p; hsa-miR-4762-3p; hsa-miR-496; hsa-miR-1233; hsa-miR-1229; PTEN- AKT1 207 hsa-miR-1915; hsa-miR-4721; hsa-miR-3162-3p; hsa-miR-4738-5p; hsa-miR-4723- 5p; AKT2 208 hsa-miR-4716-3p; hsa-miR-29b; hsa-miR-4278; hsa-miR-3943; hsa-miR-3065-3p; PTEN 5728 hsa-miR-642b; hsa-miR-486-5p; hsa-miR-148a; hsa-miR-3944-5p; hsa-miR-3691-5p; Modulators TSC1 7248 hsa-miR-130a; hsa-miR-1537; hsa-miR-637; hsa-miR-3141; hsa-miR-3684; MTKPT TSC2 7249 hsa-miR-4420; hsa-miR-654-3p; hsa-miR-4722-5p; hsa-miR-615-5p; hsa-miR-3922- 5p; STK11 6794 hsa-miR-663; hsa-miR-744; hsa-miR-4723-5p; hsa-miR-3960; hsa-miR-615-5p; PIM1 5292 hsa-miR-4749-3p; hsa-miR-761; hsa-miR-3689a-3p; hsa-miR-331-3p; hsa-miR- 4436b-3p; PIM2 11040 hsa-miR-361-3p; hsa-miR-4532; hsa-miR-3654; hsa-miR-4645-5p; hsa-miR-4768-3p; PIM3 415116 hsa-miR-3195; hsa-miR-4697-5p; hsa-miR-654-5p; hsa-miR-4467; hsa-miR-637; RAS KRAS 3845 hsa-miR-3923; hsa-miR-4323; hsa-miR-4447; hsa-miR-513a-5p; hsa-miR-548ag; NRAS 4893 hsa-miR-502-5p; hsa-miR-1296; hsa-miR-1324; hsa-miR-3120-3p; hsa-miR-4271; HRAS 3265 hsa-miR-3667-3p; hsa-miR-4728-5p; hsa-miR-4292; hsa-miR-4532; hsa-miR-663; RAF RAF1 5894 hsa-miR-1291; hsa-miR-7; hsa-miR-3126-5p; hsa-miR-296-5p; hsa-miR-764; BRAF 673 hsa-miR-617; hsa-miR-2110; hsa-miR-3977; hsa-miR-1182; hsa-miR-1289; TELOMERASE TERT 7015 hsa-miR-4650-5p; hsa-miR-491-5p; hsa-miR-4651; hsa-miR-3687; hsa-miR-4292; TERC 7012 TEP1 7011 hsa-miR-1911; hsa-miR-3132; hsa-miR-136; hsa-miR-2861; hsa-miR-31; HSP90AA1 3320 hsa-miR-4753-5p; hsa-miR-632; hsa-miR-519e; hsa-miR-3679-3p; hsa-miR-134; DKC1 1736 hsa-miR-3194-3p; hsa-miR-621; hsa-miR-3620; hsa-miR-646; hsa-miR-4279; PTGES3 10728 hsa-miR-3189-5p; hsa-miR-3135; hsa-miR-4266; hsa-miR-3678-3p; hsa-miR-4286; IGF & Warburg IGF1 3479 hsa-miR-483-3p; hsa-miR-1275; hsa-miR-4435; hsa-miR-488; hsa-miR-625; IGF2 3481 hsa-miR-4447; hsa-miR-491-5p; hsa-miR-210; hsa-miR-3191; hsa-miR-3144-5p; IGF1R 3480 hsa-miR-4746-3p; hsa-miR-4784; hsa-miR-4763-3p; hsa-miR-4327; hsa-miR-3157- 5p; IGF2R 3482 hsa-miR-4667-3p; hsa-miR-653; hsa-miR-4707-3p; hsa-miR-4736; hsa-miR-548an; INSR 3643 hsa-miR-2467-5p; hsa-miR-3975; hsa-miR-3188; hsa-miR-4707-3p; hsa-miR-4290; IRS1 3667 hsa-miR-660; hsa-miR-541; hsa-miR-4462; hsa-miR-544b; hsa-miR-183; PKM2 5315 hsa-miR-762; hsa-miR-625; hsa-miR-612; hsa-miR-4675; hsa-miR-4665-5p; WNT CDH1 999 hsa-miR-4640-3p; hsa-miR-4711-5p; hsa-miR-3689c; hsa-miR-2355-5p; hsa-miR- 1296; CTNNA1 1495 hsa-miR-1288; hsa-miR-4440; hsa-miR-4515; hsa-miR-4705; hsa-miR-9; CTNNB1 1499 hsa-miR-3688-5p; hsa-miR-3162-3p; hsa-miR-4776-5p; hsa-miR-4496; hsa-miR- 3619-3p; WNT1 7471 hsa-miR-4488; hsa-miR-4784; hsa-miR-4695-5p; hsa-miR-4644; hsa-miR-4689; FZD1 8321 hsa-miR-4269; hsa-miR-4769-5p; hsa-miR-1275; hsa-miR-1324; hsa-miR-4279; WNT5A 7474 hsa-miR-2110; hsa-miR-4691-5p; hsa-miR-876-5p; hsa-miR-3127-3p; hsa-miR-4656; WNT5B 81029 hsa-miR-4316; hsa-miR-4258; hsa-miR-2909; hsa-miR-1296; hsa-miR-486-3p; FZD5 7855 hsa-miR-296-5p; hsa-miR-3943; hsa-miR-188-3p; hsa-miR-3661; hsa-miR-3672; WIF1 11197 hsa-miR-1972; hsa-miR-3938; hsa-miR-548v; hsa-miR-140-3p; hsa-miR-3977; DKK1 22943 hsa-miR-493; hsa-miR-4639-3p; hsa-miR-4727-5p; hsa-miR-4678; hsa-miR-934; PARP PARP1 142 hsa-miR-891b; hsa-miR-4536; hsa-miR-4451; hsa-miR-555; hsa-miR-7; BRCA1 672 hsa-miR-615-5p; hsa-miR-3667-3p; hsa-miR-4446-3p; hsa-miR-760; hsa-miR-4656; XRCC1 7515 hsa-miR-589; hsa-miR-4477a; RAD54L 8438 hsa-miR-4713-5p; hsa-miR-1225-3p; hsa-miR-3918; hsa-miR-3667-3p; hsa-miR- 1291; RAD54B 25788 hsa-miR-587; hsa-miR-4268; hsa-miR-548s; hsa-miR-3926; hsa-miR-1; ATM 472 hsa-miR-892b; hsa-miR-193a-3p; hsa-miR-4735-3p; hsa-miR-4736; hsa-miR-4262; ATR 545 hsa-miR-3613-5p; hsa-miR-383; hsa-miR-4760-5p; hsa-miR-140-3p; hsa-miR-586; CHEK1 1111 hsa-miR-2355-5p; hsa-miR-541; hsa-miR-1286; hsa-miR-4733-3p; hsa-miR-16; CHEK2 11200 hsa-miR-3118; hsa-miR-759; hsa-miR-4276; hsa-miR-3938; hsa-miR-943; WEE1 7465 hsa-miR-4716-3p; hsa-miR-4723-5p; hsa-miR-424; hsa-miR-3120-3p; hsa-miR-4278; HDAC HDAC1 3065 has-miR-4284; hsa-miR-4292; hsa-miR-4271; hsa-miR-3126-5p; hsa-miR-584; HDAC2 3066 hsa-miR-362-5p; hsa-miR-3977; hsa-miR-3194-3p; hsa-miR-4662a-5p; hsa-miR- 4720-5p; HDAC3 8841 hsa-miR-3189-3p; hsa-miR-1261; hsa-miR-326; hsa-miR-1302; hsa-miR-4308; HDAC4 9759 hsa-miR-4292; hsa-miR-4313; hsa-miR-4728-5p; hsa-miR-1225-3p; hsa-miR-4316; HDAC5 10014 hsa-miR-331-3p; hsa-miR-671-5p; hsa-miR-4498; hsa-miR-296-5p; hsa-miR-4505; JAK-STAT JAK1 3716 hsa-miR-4252; hsa-miR-4437; hsa-miR-4520a-3p; hsa-miR-323b-5p; hsa-miR-4674; JAK2 3717 hsa-miR-4720-5p; hsa-miR-4468; hsa-miR-3120-3p; hsa-miR-4777-3p; hsa-miR-568; STAT1 6772 hsa-miR-4682; hsa-miR-1252; hsa-miR-3119; hsa-miR-4697-3p; hsa-miR-2682; STAT2 6773 hsa-miR-665; hsa-miR-3202; hsa-miR-4292; hsa-miR-4313; hsa-miR-1289; STAT3 6774 hsa-miR-1299; hsa-miR-4753-5p; hsa-miR-1184; hsa-miR-874; hsa-miR-5047; SOCS1 8651 hsa-miR-4645-5p; hsa-miR-556-3p; hsa-miR-331-3p; hsa-miR-4716-3p; hsa-miR- 324-5p; HEDGEHOG SHH 6469 hsa-miR-1471; hsa-miR-4749-3p; hsa-miR-4313; PTCH1 5727 hsa-miR-4757-5p; hsa-miR-564; hsa-miR-1262; hsa-miR-767-3p; hsa-miR-125a-3p; SMO 6608 hsa-miR-370; hsa-miR-4690-3p; hsa-miR-4758-3p; hsa-miR-423-3p; hsa-miR-1915; STK36 27148 hsa-miR-571; hsa-miR-3192; hsa-miR-581; hsa-miR-920; hsa-miR-4715-5p; PRKACA 5566 hsa-miR-4723-5p; hsa-miR-4665-5p; hsa-miR-608; hsa-miR-423-5p; hsa-miR-625; SUFU 51684 hsa-miR-3184; hsa-miR-4487; hsa-miR-4688; hsa-miR-4728-5p; hsa-miR-4741; GLI1 2735 hsa-miR-3943; hsa-miR-4279; hsa-miR-4292; hsa-miR-361-3p; hsa-miR-4533; DNA REPAIR ERCC1 2067 hsa-miR-661; hsa-miR-1913; hsa-miR-323-5p; hsa-miR-1972; hsa-miR-1268; RAD52 5893 hsa-miR-3922-3p; hsa-miR-4725-3p; hsa-miR-342-3p; hsa-miR-542-3p; hsa-miR- 4303; XRCC4 7518 hsa-miR-361-5p; hsa-miR-380; hsa-miR-4520a-3p; hsa-miR-3121-5p; hsa-miR- 2355-3p; RAD51 5888 hsa-miR-198; hsa-miR-532-3p; hsa-miR-606; hsa-miR-4430; hsa-miR-4432; BRCA1 672 hsa-miR-615-5p; hsa-miR-3667-3p; hsa-miR-4446-3p; hsa-miR-760; hsa-miR-4656; NEDD8 4738 hsa-miR-4713-3p; hsa-miR-4726-5p; hsa-miR-665; hsa-miR-1285; hsa-miR-1322; NAE1 8883 hsa-miR-4524; hsa-miR-646; hsa-miR-4660; hsa-miR-582-5p; hsa-miR-603; NOTCH NOTCH1 4851 hsa-miR-4313; hsa-miR-4268; hsa-miR-449a; hsa-miR-139-5p; hsa-miR-4727-5p; Adam17 6868 hsa-miR-507; hsa-miR-3918; hsa-miR-4687-5p; hsa-miR-3651; hsa-miR-1827; PSEN1 5663 hsa-miR-3065-3p; hsa-miR-4697-3p; hsa-miR-3120-5p; hsa-miR-4303; hsa-miR-488; NCSTN 23385 hsa-miR-339-5p; hsa-miR-4654; hsa-miR-1321; hsa-miR-4648; hsa-miR-3657; JAG1 182 hsa-miR-4692; hsa-miR-1273g; hsa-miR-920; hsa-miR-4661-5p; hsa-miR-4283; SRRT 51593 hsa-miR-4700-3p; hsa-miR-3190; hsa-miR-487b; hsa-miR-520f; hsa-miR-3929; APH1A 51107 hsa-miR-3679-3p; hsa-miR-198; hsa-miR-3173-3p; hsa-miR-4685-5p; hsa-miR-3131; Others ROS1 6098 hsa-miR-4693-3p; hsa-miR-4653-3p; hsa-miR-33a; hsa-miR-606; hsa-miR-3659; ALK 238 hsa-miR-642a; hsa-miR-646; hsa-miR-4764-3p; hsa-miR-1271; hsa-miR-4713-3p; RET 5979 hsa-miR-544; hsa-miR-4652-5p; hsa-miR-510; hsa-miR-31; hsa-miR-3622b-5p; UBA1 7317 hsa-miR-4716-3p; hsa-miR-762; hsa-miR-4640-5p; hsa-miR-3202; hsa-miR-31;

indicates data missing or illegible when filed

TABLE 12 Mutational status KRAS EFGR PIK3CA BRAF ERBB2 P53 1 c.34G > K WT WT WT WT 80_SNP_A > G_R-Arg_exon6, p.Gly12Cys 102_deletion_C_exon8 (G12C) 2 c.35G > K WT WT WT WT 39_G > A_Met > Ile_exon7, p.Gly12Val 75_G > C_exon7 (G12V) 3 WT WT WT WT WT 47_G > T_Ser > Ile_exon7, 51_C > A_Ser > Ser_exon7 7 WT WT WT WT c.2883T > G WT p.Ile961Met (1961M) AGVGD: Class C0_exon 24 8 c.34G > K WT WT WT WT WT p.Gly12Cys (G12C) 12 c.35G > R WT WT WT WT WT p.Gly12Asp (G12D) 15 WT WT WT WT WT 63_C > T_Gly > Gly_exon7 20 c.34G > K WT WT WT WT WT p.Gly12Cys (G12C) 23 c.35G > K WT WT WT WT WT p.Gly12Val (G12V) 25 WT WT c.30750 > T WT WT 139_A > G_Glu > Gly_exon5 p. = rs17849079 29 c.35G > K WT WT WT WT WT p.Gly12Val (G12V) 30 WT WT WT WT WT 17_G > T_exon10 32 c.35G > R WT WT WT WT WT p.Gly12Asp (G12D) 33 WT WT WT WT WT 177_G > T_Asp > Tyr_exon5 34 WT WT WT WT WT 96_G > C_Val > Leu_exon5 36 WT WT nd WT 62_G > A_Gly > Asp_exon7, and 88_insertion_G_exon7 39 c.34G > K WT WT WT WT WT p.Gly12Cys (G12C) 40 c.34G > K WT WT WT WT 94_G > A_Arg > His_exon5 p.Gly12Cys (G12C) 42 WT WT WT WT WT 55_G > C_Gly > Ala_exon8 46 c.35G > K WT WT WT WT WT p.Gly12Val (G12V) 47 WT c.2184 + 19G > R WT WT WT 57_A > T_Arg > Stop_exon8 Non Codant rs17337107 49 WT c.2184 + 19G > R WT WT WT WT Non Codant rs17337107 50 WT WT WT WT WT 58_insertion_G, 75_SNP_G > A_Arg > Arg_exon7 51 WT WT WT WT WT 42_A > G_Lys > Glu_exon5 57 WT c.2184 + 19G > R WT WT WT WT Non Codant rs17337107 58 WT WT c.2937- WT WT WT 96A > C Non Codant 59 WT WT WT c.1799T > W wt WT p.Val600Glu (V600E) 61 WT WT WT WT WT 58_G > A_Gly > Ser_exon6, 65_T > A_Met > Lys_exon7, 70_G > A?_Gly? > Arg?_exon7, 129_C > T_exon7 62 WT c.2184 + 19G > A WT WT WT WT Non Codant rs17337107 68 WT WT wt wt wt 47_G > T_Ser > Ile_exon7, 51_C > A_Ser > Ser_exon7, 83_C > A?_Pro? > His?_exon7 70 WT WT WT WT WT 119_G > T_Lys > Asn_exon5 71 WT c.2320_2321ins3bp (CAC) WT WT WT WT p.Val774delinsAlaLeu exon 20 72 c.35G > S WT WT WT WT 152_insertion_T_exon5 p.Gly12Ala (G12A) 74 WT c.2184 + 19G > R WT WT WT WT Non Codant rs17337107 75 WT WT WT WT WT 83_T > C_exon7 76 WT WT WT WT WT 55_A > G_Tyr > Cys_exon6 78 c.34G > K WT WT WT WT WT p.Gly12Cys (G12C) 80 WT WT WT WT WT 163_A > T_His > Leu_exon5 83 c.34G > K WT WT WT WT WT p.Gly12Cys (G12C) 84 WT WT WT WT WT 96_G > T_Val > Phe_exon5 88 WT WT WT WT WT 158_C > G_exon7 91 c.34G > K c.2184+19G > R WT WT WT 80_SNP_A > G_R-Arg_exon6, p.Gly12Cys Non Codant rs17337107 101_A > G_Glu > Gly_exon7, (G12C) 106_T > A_Ser > Thr_exon7, 142_C > G_exon7 92 WT c.2215_2229del15bp WT WT WT WT p.Lys739_Ala743de exon 20 93 WT c.2156G > C p.Gly719Ala WT WT WT WT (G719A) VAR_026086 exon 18 c.2303G > T p.Ser768Ile (S768I) AGVGD: Class C65 exon 20 94 c.34G > K WT WT WT WT WT p.Gly12Cys (G12C) 96 c.34G > K c.2184 + 19G > R WT WT WT WT p.Gly12Cys Non Codant rs17337107 (G12C) 102 WT WT WT WT WT 54_T > C_Tyr > His_exon6 103 WT c.2184 + 19G > R WT WT WT WT Non Codant rs17337107 104 c.35G > K WT WT WT WT WT p.Gly12Val (G12V) 107 WT WT WT WT WT 70_C > T_Arg > Trp_exon7, 71_SNP_G > A_exon7 108 WT WT WT WT WT 26deletion_T_exon9 111 WT c.2313_2314ins9bp (CCCCAGGCG) WT WT WT WT p.Pro772_His773insGlnAlaPro_expn 20 113 c.34G > K WT WT WT WT WT p.Gly12Cys (G12C) 114 WT WT WT WT WT WT 115 WT c.2184 + 19G > R WT WT WT WT Non Codant rs17337107 118 WT WT WT WT WT 99_C > G_Arg > Gly_exon5 121 c.183A > W WT WT WT WT 92_C > T_exon5, p.Gln61His 104_C < T_exon5, (Q61H) 128_C > G_Ser > Arg_exon8, rs17851045 exon 3

TABLE 13 Calculated scores Wherein P means Patient, (1) refers to a score calculated based on mRNA expression, (2) refers to a score calculated based on mutation and mRNA expression, (3) refers to a score calculated based on mutation, mRNA expression, and miRNA expression, and (4) refers to a score calculated based on mutation, mRNA expression, miRNA expression and Copy Number Variation. 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 1 2 3 4 P Her CDK 4-6 PLK_AURKA_Kinesins ANGIOGENESIS ANGIOPOIETINS 1 2 2 1 1 4 4 3 3 7 7 7 7 5 5 6 5 2 2 2 2 2 2 2 5 5 6 6 6 6 5 5 5 5 8 8 7 7 6 6 5 5 3 3 3 9 9 6 6 4 4 7 7 8 8 3 3 1 1 1 1 1 1 4 1 1 2 2 4 4 2 2 5 5 5 5 5 5 5 5 8 8 8 8 5 9 9 7 8 10 10 10 10 3 3 3 3 8 8 9 9 8 8 8 8 6 7 7 8 8 8 8 7 7 8 8 8 8 10 10 10 10 9 9 9 9 7 7 10 10 10 1 1 1 1 1 1 1 1 2 2 3 3 7 7 5 5 8 8 8 5 5 10 10 10 10 10 10 9 9 9 9 8 8 4 4 2 2 9 4 4 5 5 1 1 1 1 3 3 3 3 1 1 1 1 2 2 1 1 10 1 1 1 1 2 2 1 1 1 1 1 1 4 4 3 2 5 5 3 3 11 9 9 7 7 4 4 3 3 6 6 6 6 9 9 9 9 10 10 10 10 12 4 4 7 7 3 3 2 2 1 1 1 1 6 6 4 4 6 6 5 5 13 10 10 10 10 9 9 9 9 9 9 9 9 6 6 6 7 1 1 1 1 14 8 8 9 9 2 2 3 3 1 1 1 1 3 3 5 6 9 9 10 10 15 4 4 2 2 10 10 9 9 10 10 10 10 1 1 1 1 2 2 1 4 16 6 6 7 6 3 3 5 5 5 5 6 6 5 5 6 5 9 9 10 10 17 7 7 4 4 7 7 8 8 7 7 7 7 8 8 8 8 6 6 6 6 18 10 10 10 10 8 8 10 9 8 8 9 9 8 8 9 9 5 5 7 7 19 10 10 10 10 8 8 9 9 6 6 7 7 5 5 6 6 5 5 6 6 20 1 1 1 1 4 4 4 4 9 9 9 9 3 3 1 1 8 8 7 7 21 7 7 8 8 5 5 5 5 2 2 2 2 2 2 2 2 8 8 6 6 22 9 9 9 8 5 5 5 5 6 6 5 5 6 6 5 5 5 5 5 5 23 7 7 4 4 5 5 6 6 5 5 5 5 10 10 10 10 10 10 10 10 24 7 7 6 6 8 8 9 9 8 8 8 9 1 1 1 1 1 1 1 1 25 1 1 2 2 10 10 10 10 10 10 10 10 1 1 1 1 1 1 2 1 26 4 4 4 6 8 8 7 10 8 8 7 7 10 10 10 10 10 10 10 10 27 1 1 2 2 10 10 10 10 3 3 4 4 8 8 9 9 9 9 9 9 28 2 2 1 1 6 6 5 5 10 10 10 10 4 10 10 10 4 4 3 3 29 6 6 7 7 6 6 8 8 6 6 6 6 6 6 7 7 7 7 7 7 30 7 7 5 5 9 9 9 9 10 10 10 10 6 6 6 6 8 8 8 8 31 10 10 10 10 4 4 6 6 4 4 5 5 3 3 3 3 10 10 10 10 32 5 5 5 5 3 3 4 4 1 1 1 1 5 5 6 6 5 5 5 5 33 8 8 9 9 3 3 6 6 4 4 4 4 2 2 3 3 1 1 1 1 34 2 2 2 3 10 10 10 10 10 10 10 10 1 1 2 3 4 4 6 6 35 8 8 6 6 8 8 5 5 7 7 7 7 10 10 10 10 10 10 9 8 36 3 3 2 3 10 10 10 10 3 3 3 3 9 9 8 8 4 4 2 3 37 6 6 7 7 4 4 5 5 3 3 3 3 2 2 2 2 6 6 7 7 38 4 4 4 4 7 7 8 8 4 4 4 4 4 4 4 4 2 2 1 1 39 10 10 10 10 5 5 3 3 7 7 6 6 7 7 6 6 9 9 8 8 40 4 4 4 4 2 2 2 2 1 1 1 1 8 8 8 8 2 2 4 4 41 5 5 3 3 5 5 5 5 3 3 3 3 8 8 7 7 9 9 9 9 42 10 10 10 10 10 10 10 10 5 5 6 6 9 9 9 9 6 6 4 4 43 3 3 5 5 4 4 5 5 9 9 7 7 8 8 8 8 10 10 10 10 44 8 8 7 7 5 5 6 6 4 4 5 5 8 8 9 9 3 3 4 4 45 6 6 6 6 7 7 7 7 7 7 8 8 4 4 4 4 3 3 3 3 46 5 5 3 2 1 1 2 2 1 1 2 2 2 2 3 3 3 3 5 5 47 10 10 10 10 9 9 8 8 8 8 8 8 5 5 4 4 1 1 3 2 48 4 4 6 6 6 6 7 7 9 9 8 8 5 5 6 6 5 5 6 6 49 5 10 10 10 8 8 7 7 5 5 5 5 4 4 3 3 8 8 7 7 50 1 1 10 10 7 7 7 7 9 9 9 10 9 9 8 8 8 8 9 9 51 3 3 3 3 4 4 6 6 9 9 9 9 2 2 2 2 2 2 3 3 52 8 8 7 7 4 4 7 7 1 1 1 1 1 10 10 10 2 2 4 4 53 3 3 3 3 2 2 1 1 3 3 4 4 2 2 2 2 3 3 5 5 54 9 9 9 9 1 1 1 1 2 2 2 2 3 3 3 3 6 6 6 6 55 7 7 8 10 5 5 4 4 4 4 4 4 7 7 7 7 9 9 9 8 56 9 9 8 9 3 3 4 4 7 7 8 8 5 5 6 6 7 7 8 8 57 4 10 10 10 9 9 9 9 8 8 8 8 7 7 7 7 6 6 5 5 58 10 10 9 9 3 3 6 6 2 2 2 2 4 4 4 4 6 6 4 4 59 9 10 10 10 7 7 7 7 2 2 2 2 2 2 3 3 8 8 7 7 60 9 9 9 9 1 1 2 2 1 1 1 1 2 2 3 3 3 3 6 6 61 4 4 3 3 4 4 2 2 9 9 8 8 10 10 10 10 9 9 8 9 62 8 10 10 10 8 8 6 6 9 9 8 8 5 5 5 6 1 1 2 2 63 6 6 8 8 3 3 3 3 3 3 4 4 2 10 10 10 7 7 7 7 64 2 2 1 1 9 9 7 7 5 5 6 6 10 10 9 9 9 9 8 8 65 3 3 3 3 6 6 4 4 5 5 4 4 3 3 2 2 3 3 2 2 66 1 1 1 1 2 2 2 2 1 1 1 1 5 5 5 5 7 7 6 6 67 7 7 7 7 1 1 1 1 2 2 2 2 9 9 8 8 4 4 6 6 68 6 10 10 10 1 1 1 1 6 6 7 7 3 3 3 3 2 2 2 2 69 1 1 4 4 1 1 4 4 2 2 2 2 8 8 9 9 6 6 8 8 70 10 10 10 9 8 8 8 8 6 6 6 6 10 10 10 10 4 4 3 3 71 6 10 10 10 1 1 1 1 4 4 3 3 7 7 8 8 8 8 8 9 72 5 5 6 6 5 5 7 7 2 2 3 3 10 10 10 10 9 9 9 9 73 10 10 10 10 8 8 8 8 10 10 10 10 1 1 1 1 10 10 10 10 74 2 10 10 10 9 9 9 9 10 10 10 10 1 1 1 1 4 4 4 3 75 10 10 8 8 7 7 5 5 7 7 7 7 10 10 10 10 7 7 4 4 76 3 3 8 7 10 10 10 9 8 8 9 9 7 7 8 8 4 4 4 4 77 1 1 1 1 3 3 2 2 2 2 2 2 6 6 5 5 7 7 6 6 78 8 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3 3 3 10 10 10 65 6 4 4 2 2 5 6 6 5 1 1 9 9 9 9 9 9 66 1 1 1 1 1 1 1 1 2 1 1 9 9 9 4 4 2 67 2 2 2 3 2 2 1 1 1 4 4 3 4 4 4 4 3 68 7 6 6 1 1 8 5 5 2 5 5 8 9 9 2 2 1 69 2 4 4 2 4 1 2 2 1 4 4 2 4 4 3 3 5 70 3 1 1 7 4 3 3 3 7 7 7 1 1 1 1 1 1 71 5 8 8 2 3 7 1 1 4 6 6 10 10 10 6 6 7 72 8 8 10 3 4 3 5 5 1 2 2 3 3 3 3 3 3 73 9 10 10 5 6 10 10 10 9 10 10 3 4 4 10 10 10 74 2 2 2 6 7 9 7 7 5 5 5 10 10 10 9 9 9 75 10 10 10 6 3 6 5 5 8 7 9 4 4 3 8 8 7 76 2 2 2 1 1 9 9 9 8 9 9 1 2 2 3 3 3 77 5 3 3 1 1 6 4 4 1 1 1 9 8 8 6 6 5 78 5 7 6 8 7 8 6 6 1 2 2 7 7 7 2 2 2 79 10 10 10 2 2 10 10 10 10 10 10 1 1 1 10 10 10 80 1 1 1 4 6 9 8 7 6 2 2 8 5 5 9 9 9 81 5 5 5 7 6 3 3 3 2 3 3 1 1 1 4 4 4 82 6 4 4 2 3 1 4 4 3 3 3 6 6 6 6 6 6 83 9 8 8 9 8 7 7 7 2 1 1 8 7 7 3 3 2 84 8 8 8 3 3 3 3 3 9 10 10 2 2 2 5 5 5 85 7 6 6 8 7 4 4 4 6 3 3 2 2 2 7 7 7 86 5 6 6 7 9 4 7 7 8 8 7 8 7 7 9 9 10 87 7 8 7 3 3 7 7 7 3 4 4 5 5 5 5 5 6 88 2 1 1 2 2 8 8 8 10 9 9 10 9 9 1 1 2 89 6 8 8 4 5 7 10 10 7 8 8 9 9 9 6 6 6 90 1 1 1 7 9 10 1 1 5 8 8 6 7 7 1 1 2 91 4 6 6 4 5 2 3 3 4 9 9 2 4 4 3 3 4 92 7 6 6 10 10 3 6 6 7 6 5 10 10 10 6 6 6 93 2 2 2 6 5 3 2 2 3 2 2 7 8 8 1 1 1 94 7 5 5 5 4 1 1 1 8 8 8 1 1 1 2 2 1 95 3 3 3 7 7 9 7 7 10 9 9 3 3 3 1 1 1 96 4 3 3 4 3 2 2 2 3 1 1 4 4 4 2 2 1 97 10 9 9 2 1 4 4 4 7 3 3 8 8 8 7 7 7 98 2 2 2 1 1 2 2 2 2 2 2 6 6 6 4 4 4 99 7 7 7 2 1 4 4 4 8 10 10 2 1 1 7 7 6 100 8 8 8 10 9 8 9 8 8 8 8 1 2 2 10 10 10 101 7 7 7 7 6 2 4 4 3 3 3 2 3 3 1 1 1 102 5 4 7 1 1 10 9 9 10 10 10 1 1 1 7 7 6 103 3 4 4 8 7 8 8 8 10 10 10 7 8 10 6 6 4 104 2 6 6 1 2 6 6 6 5 5 5 10 10 10 7 7 8 105 6 7 7 7 8 5 9 9 4 3 3 5 6 6 7 7 7 106 7 7 7 10 10 1 1 9 8 8 6 6 6 5 5 6 107 6 4 4 5 4 9 7 7 9 10 10 1 1 1 10 10 10 108 8 8 8 6 5 3 2 2 7 4 4 5 5 5 6 6 5 109 9 9 9 10 9 2 3 3 5 5 5 6 5 5 2 2 3 110 3 2 2 8 9 7 8 9 7 7 7 5 6 5 10 10 10 111 7 6 6 9 9 8 9 9 6 9 9 2 3 3 8 8 8 112 5 4 4 10 10 6 7 8 9 8 8 5 3 3 10 10 10 113 4 3 3 9 8 7 5 5 5 4 4 4 4 4 3 3 3 114 9 9 9 7 8 5 6 6 3 5 5 5 5 4 7 7 7 115 7 7 7 2 3 5 7 7 4 7 7 8 9 9 5 5 4 116 1 1 1 6 7 10 10 9 10 9 9 4 4 4 10 10 10 117 8 6 6 9 9 9 8 8 4 5 5 7 8 8 4 4 4 115 4 5 5 5 7 6 8 8 3 5 5 6 7 7 8 8 8 119 3 3 3 10 10 8 9 9 8 8 8 10 10 10 8 8 8 120 2 2 2 2 2 7 6 6 3 2 5 9 10 9 3 3 3 121 8 8 8 9 9 3 3 3 9 9 9 9 9 9 4 4 5 1 2 4 1 2 4 1 2 3 4 1 2 3 4 1 2 3 4 DNA_REPAIR NOTCH OTHERS PDL1 CTLA4 1 6 6 6 1 1 1 8 8 7 7 3 3 9 9 9 9 9 9 2 7 7 7 8 8 7 3 3 2 2 9 9 10 10 10 10 9 9 3 10 10 10 6 6 4 6 6 4 4 7 7 1 1 6 6 4 4 4 4 4 4 8 8 8 5 5 4 4 10 10 9 9 4 4 2 2 5 2 2 2 7 7 5 9 9 8 8 7 7 2 2 10 10 10 10 6 8 8 8 10 10 10 8 8 9 9 9 9 7 7 2 2 6 10 7 1 1 1 2 2 1 7 7 6 6 4 4 5 5 6 6 3 3 8 6 6 5 6 6 4 9 9 9 9 8 8 10 10 9 9 8 8 9 4 4 3 7 7 6 1 1 1 1 6 6 6 5 7 7 7 7 10 1 1 1 2 2 1 4 4 4 4 5 5 10 10 9 9 5 5 11 5 5 4 6 6 8 10 10 10 10 4 4 8 8 9 9 8 8 12 1 1 1 2 2 1 5 5 4 4 1 1 4 4 3 3 2 2 13 9 9 8 7 7 7 5 5 5 5 7 7 3 3 8 8 8 8 14 1 1 1 4 4 6 1 1 2 2 5 5 3 3 5 5 7 6 15 10 10 9 8 8 8 1 1 1 1 6 6 4 4 2 2 1 1 16 6 6 7 1 1 3 4 4 5 5 3 3 7 6 10 10 10 10 17 5 5 4 4 4 5 9 9 9 9 6 6 6 6 10 10 10 10 18 7 7 8 1 1 6 8 8 9 9 10 10 10 10 6 6 9 8 19 5 5 4 5 5 4 10 10 10 10 9 9 3 3 5 5 7 7 20 6 6 5 1 1 1 9 9 9 9 3 3 2 2 4 4 4 4 21 3 3 4 3 3 2 3 3 2 2 4 4 1 1 6 6 4 4 22 6 6 4 3 3 2 2 2 1 1 7 7 5 5 7 7 6 6 23 4 4 7 2 2 4 3 3 6 6 10 10 7 7 9 9 9 9 24 8 8 9 6 6 8 6 6 8 8 2 2 6 6 5 5 7 7 25 9 9 10 8 8 10 10 10 10 10 2 2 1 1 1 1 5 5 26 7 7 7 10 10 9 7 7 7 7 8 8 9 9 8 8 10 9 27 3 3 4 6 6 8 7 7 9 9 9 9 9 9 8 8 10 10 28 10 10 10 9 9 9 1 1 1 1 2 2 7 7 8 8 7 7 29 4 4 6 3 3 5 3 3 6 6 10 10 9 9 9 9 10 10 30 6 6 5 10 10 10 8 8 8 8 6 6 5 4 4 4 3 3 31 7 7 8 3 3 4 6 6 6 6 8 8 8 8 6 6 7 7 32 1 1 1 1 1 2 7 7 8 8 5 5 5 5 5 5 5 5 33 4 4 3 5 5 3 7 7 6 6 6 6 5 5 4 4 5 5 34 10 10 10 10 10 10 1 2 2 8 8 3 10 3 3 5 5 35 8 8 8 10 10 10 10 10 10 10 2 2 10 10 5 5 4 4 36 4 4 5 1 1 1 4 4 3 3 1 1 5 5 3 3 1 1 37 2 2 2 4 4 6 4 4 4 4 8 8 4 4 6 6 7 7 38 3 3 3 7 7 6 10 10 10 10 4 4 5 5 2 2 2 2 39 8 8 8 7 7 6 3 3 3 3 7 7 6 6 10 10 9 9 40 2 2 2 2 2 2 3 3 3 3 3 3 7 7 3 3 5 5 41 4 4 4 5 5 3 7 7 7 7 5 5 3 3 3 3 3 3 42 3 3 2 9 9 8 10 10 9 9 9 9 10 10 9 9 8 8 43 9 9 9 4 4 3 8 8 8 8 2 2 3 3 1 1 2 2 44 5 5 6 3 3 4 2 2 3 3 7 7 4 4 5 5 6 6 45 8 8 7 8 8 9 6 6 5 5 10 10 10 10 6 6 6 6 46 3 3 6 4 4 4 7 7 7 7 6 6 5 5 7 7 7 7 47 9 9 9 10 10 10 2 2 3 3 9 9 1 1 2 2 3 3 48 9 9 9 9 9 10 1 1 1 1 10 10 8 8 5 5 6 6 49 9 9 8 9 9 8 9 9 8 8 10 10 8 8 10 10 9 8 50 5 5 6 1 1 1 4 4 4 4 1 1 9 9 10 10 10 10 51 8 8 9 8 8 8 4 4 7 7 10 10 4 4 7 7 7 7 52 3 3 6 4 4 6 10 10 10 10 6 6 3 3 2 2 4 4 53 6 6 7 3 3 3 1 1 1 1 6 6 6 6 7 7 6 6 54 2 2 2 3 3 3 5 5 5 5 2 2 1 1 3 3 3 3 55 4 4 3 3 3 2 7 7 6 6 6 6 4 4 2 2 2 2 56 6 6 5 9 9 9 5 5 6 6 1 1 1 1 1 1 1 1 57 6 6 7 4 4 3 9 9 9 9 9 9 8 8 8 8 9 9 58 2 2 2 2 2 2 4 4 3 3 8 8 2 2 9 9 8 7 59 2 2 2 9 9 9 8 8 9 9 6 6 2 2 4 4 4 4 60 1 1 2 4 4 5 8 8 8 8 3 3 2 2 2 2 6 6 61 8 8 5 10 10 10 3 3 2 2 2 2 3 3 3 3 1 1 62 10 10 10 10 10 10 5 5 4 4 7 7 3 3 1 1 2 2 63 3 3 3 6 6 7 10 10 10 10 7 7 4 4 4 4 7 6 64 6 6 6 4 4 7 10 10 10 10 3 3 4 4 1 1 1 1 65 7 7 6 7 7 5 2 2 1 1 7 7 3 3 6 6 4 4 66 1 1 1 5 5 2 3 3 3 3 10 10 6 6 7 7 5 5 67 1 1 1 3 3 2 1 1 1 1 3 3 9 8 6 6 6 6 68 6 6 7 5 5 3 3 3 3 3 8 8 10 10 9 9 5 5 69 2 2 5 2 2 6 1 1 2 2 8 8 9 9 5 5 9 9 70 4 4 3 7 7 5 9 9 8 8 2 2 2 2 2 2 1 1 71 7 7 8 5 5 5 6 6 6 6 7 7 4 4 8 8 10 9 72 1 1 1 2 2 1 3 3 5 5 3 3 3 3 3 3 4 4 73 10 10 10 1 1 5 10 10 10 10 3 3 8 8 10 10 10 10 74 8 8 8 6 6 5 1 1 1 1 10 10 10 10 10 10 10 10 75 5 5 7 10 10 9 6 6 5 5 4 4 5 5 2 2 1 1 76 9 9 9 8 8 9 2 2 2 2 3 3 2 2 1 1 3 3 77 7 7 7 2 2 1 3 3 3 3 10 10 7 7 8 8 4 4 78 9 9 9 1 1 1 5 5 5 5 9 9 2 2 10 10 9 9 79 9 9 9 3 3 5 6 6 7 7 1 1 1 1 1 1 1 1 80 10 10 10 10 10 10 2 2 2 2 5 5 1 1 4 4 3 3 81 2 2 2 1 1 1 4 4 3 3 5 5 2 2 5 5 6 6 82 2 2 3 5 5 5 2 2 2 2 5 5 6 6 7 7 8 8 83 8 8 6 6 6 4 2 2 2 2 10 10 6 6 5 5 4 4 84 4 4 4 6 6 6 9 9 9 9 1 1 7 7 1 1 1 1 85 8 8 7 8 8 6 4 4 3 3 1 1 3 3 6 6 4 4 86 8 8 8 7 7 7 9 9 10 10 2 2 4 4 6 6 8 8 87 5 5 5 1 1 2 5 5 5 6 6 6 6 6 6 7 7 88 9 9 9 6 6 9 9 8 8 5 5 6 6 4 4 5 5 89 8 8 8 4 4 7 10 10 10 10 4 4 9 9 7 7 9 9 90 10 10 10 5 5 7 6 6 6 6 7 7 4 4 9 9 3 8 91 1 1 2 6 6 6 4 4 4 4 4 4 9 9 1 1 4 4 92 5 5 5 9 9 8 10 10 10 10 4 4 5 5 7 7 6 6 93 3 3 3 5 5 4 6 6 6 6 7 7 8 7 8 8 8 7 94 2 2 1 6 6 4 2 2 2 2 1 1 1 1 1 1 1 1 95 10 10 10 9 9 9 4 4 4 4 2 2 1 1 2 2 2 2 96 1 1 1 4 4 6 5 5 4 4 4 4 2 2 3 3 2 2 97 3 3 1 7 7 5 6 6 5 5 5 5 8 8 7 7 3 3 98 2 2 3 2 2 2 6 6 7 7 9 9 7 7 8 8 8 8 99 5 5 4 9 9 8 5 5 4 4 3 3 5 5 4 4 2 2 100 10 10 10 10 10 10 6 6 5 5 5 5 2 2 2 2 2 2 101 1 1 2 5 5 4 9 9 9 9 1 1 8 8 2 2 3 3 102 9 9 9 2 2 4 7 7 7 7 1 1 8 8 4 4 6 5 103 9 9 9 9 9 9 8 8 8 8 2 2 6 6 5 5 5 10 104 5 5 8 7 7 8 8 8 9 9 9 9 10 10 9 9 10 10 105 4 4 5 8 8 9 3 3 7 7 3 3 5 5 8 8 9 9 106 4 4 5 9 9 9 1 1 1 1 6 6 8 8 1 1 3 3 107 7 7 2 10 10 10 1 1 1 1 1 1 1 1 3 3 1 1 108 5 5 5 8 8 7 8 8 8 8 8 8 7 7 3 3 2 2 109 2 2 1 5 5 3 9 9 8 8 9 9 6 6 8 8 7 7 110 10 10 10 10 10 10 5 5 6 6 8 8 7 7 5 5 5 5 111 7 7 6 3 3 2 7 7 7 7 1 1 7 7 3 3 1 1 112 6 6 4 8 8 8 2 2 1 1 8 8 2 2 4 4 3 3 113 7 7 6 1 1 1 8 8 7 7 4 4 4 3 8 8 6 6 114 3 3 3 7 7 7 2 2 3 3 4 4 8 8 4 4 3 3 115 3 3 3 5 5 3 7 7 5 5 4 4 10 10 9 9 8 8 116 10 10 10 4 4 3 8 8 6 6 2 2 1 1 10 10 9 9 117 5 5 4 8 8 7 2 2 2 2 9 9 9 9 7 7 5 5 118 7 7 6 2 2 3 7 7 7 7 5 5 10 9 10 10 10 10 119 10 10 10 9 9 9 5 5 5 5 10 10 10 10 7 7 8 8 120 7 7 7 3 3 2 4 4 4 4 8 8 7 7 10 10 10 10 121 3 3 3 7 7 7 10 10 10 10 5 5 9 9 1 1 2 2 

1-16. (canceled)
 17. A method for determining in a patient having a cancer a classification of intervention points according to their activation status, wherein: the intervention points comprise HER, CDK4,6, PLK/AURK/Kinesins, Angiogenesis, Angiopoietins, Immune Modulators, PI3K, MET, MEK, ERK, Anti-Apoptosis, FGF, mTOR, Ras/Raf, Telomerase, IGF/glycolysis, Wnt, PARP, HDAC, JAK-STAT, Hedgehog, NOTCH pathway, DNA Repair and Others', or any subgroup thereof of at least 10 intervention points, and the genes of each intervention point are defined according to Table 1 or 9; and the method comprises: characterizing a tumor sample in comparison to a normal histologically matched sample from the same patient, including: for each pathway of the group or subgroup of intervention points, determining the mRNA expression level of the genes of the intervention point as disclosed in Table 1 or 9, thereby determining a fold change of mRNA expression of tumor vs normal, (referred as mRNA TvN fold change); wholly or partially sequencing genes of Table 1 or 9, thereby identifying the presence of activating mutation in the tumor sample; optionally, for each intervention point of the group or subgroup of intervention points, determining the level of miRNAs of the genes of the intervention point as disclosed in Table 1 or 9, thereby determining a fold change of miRNAs level of tumor vs normal, (referred as miRNA TvN fold change); and optionally, for each intervention point of the group or subgroup of intervention points, determining the copy number variation of the genes of the intervention point as disclosed in Table 1 or 9, thereby determining a tumor vs normal fold change for the amplified genes; calculating a score for each pathway based on the characterization data, wherein: if, in the tumor sample, the presence of an activating mutation of a gene of an intervention point is detected, then a maximal score is given to the intervention point, in particular a score of 10 if the scoring is from 1 to 10; a score is calculated based on the arithmetic mean of the mRNA TvN fold changes of the genes for each intervention point of the group or subgroup of intervention points, provided that the mRNA TvN fold change of a gene is taken into consideration only if its value is at least 1.3; and the score of each intervention point of the group or subgroup of intervention points is either: a) the sum of the score due to the presence of an activating mutation and the score calculated by the average of the mRNA TvN fold changes; or b) the score due to the presence of an activating mutation if there is a mutation or the score calculated based on the arithmetic mean of the mRNA TvN fold changes in absence of mutation; and classifying the intervention points according to the calculated scores.
 18. The method according to claim 17, wherein the genes of Table 10 are sequenced for detecting the presence of mutations as defined in Table 10 and the p53 gene is sequenced.
 19. The method according to claim 17, wherein, for each intervention point of the group or subgroup of intervention points, the method comprises determining the miRNAs level of the genes of the pathway as disclosed in Table 1 or 9 or
 11. 20. The method according to claim 19, wherein, before the step of score calculation, a mean miRNAs fold change for each gene is calculated as the average of the miRNA TvN fold changes for the gene, a corrected mRNA TvN fold change is calculated by dividing the mRNA fold change Tumor versus Normal of the gene (mRNA TvN fold change) by the mean fold change for the miRNAs of the gene (mean miRNA TvN fold change), and the corrected mRNA TvN fold change of the gene is then used to calculate the arithmetic mean of the mRNA TvN fold changes of the genes for each intervention point.
 21. The method according to claim 19, wherein the level of miRNAs is determined and used to calculate a corrected mRNA TvN fold change for the genes of the following intervention points: mTOR-AKT-PTEN, RAS, ERK, PI3K and Immune Modulators.
 22. The method according to claim 17, wherein for each intervention point of the group or subgroup of intervention points, the method comprises determining the copy number variation of the genes of the pathway as disclosed in Table 1 or
 9. 23. The method according to claim 22, wherein, before the step of score calculation, a corrected mRNA TvN fold change of a gene of an intervention point is calculated by multiplying the mRNA TvN fold change of the gene by the CNV fold change of the gene, and the corrected mRNA TvN fold change of the gene is then used to calculate the arithmetic mean of the mRNA TvN fold changes of the genes for each intervention point.
 24. The method according to claim 17, wherein the subgroup of intervention points is: Her, CDK4,6, PLK/AURK/Kinesins, Angiogenesis, Immune Modulators, PI3K, MET, MEK, ERK, Anti-Apoptosis, FGF, mTOR, Ras/Raf, IGF/glycolysis, Wnt, PARP, and DNA Repair.
 25. The method according to claim 17, wherein the method further comprises selecting a group of three activated or disturbed intervention points in a patient having a cancer, wherein three intervention points are the three intervention points having the highest scores.
 26. A method for selecting a combination of three drugs useful for treating a patient having a cancer, wherein a group of three activated or disturbed intervention points are selected by the method of claim 25 and a drug is selected for each or disturbed intervention point, thereby providing a combination of three drugs.
 27. A method of measuring pathway activation comprising measuring the mRNA expression level of the genes of Table 1 or 9 for intervention points comprising HER, CDK4,6, PLK/AURK/Kinesins, Angiogenesis, Angiopoietins, Immune Modulators, PI3K, MET, MEK, ERK, Anti-Apoptosis, FGF, mTOR, Ras/Raf, Telomerase, IGF/glycolysis, Wnt, PARP, HDAC, JAK-STAT, Hedgehog, NOTCH pathway, DNA Repair and Others', or any subgroup thereof of at least 10 intervention points.
 28. The method according to claim 27, said method further comprising detecting the gene mutations of Table
 10. 29. The method according to claim 27, said method further comprising measuring the miRNA level of miRNA of Table 11 for intervention points comprising HER, CDK4,6, PLK/AURK/Kinesins, Angiogenesis, Angiopoietins, Immune Modulators, PI3K, MET, MEK, ERK, Anti-Apoptosis, FGF, mTOR, Ras/Raf, Telomerase, IGF/glycolysis, Wnt, PARP, HDAC, JAK-STAT, Hedgehog, NOTCH, DNA Repair and Others', or any subgroup thereof of at least 10 intervention points.
 30. The method according to claim 27, said method comprising determining the copy number variation of the genes of Table 1 or 9 for pathways comprising the group consisting of the HER, CDK4,6, PLK/AURK/Kinesins, Angiogenesis, Angiopoietins, Immune Modulators, PI3K, MET, MEK, ERK, Anti-Apoptosis, FGF, mTOR, Ras/Raf, Telomerase, IGF/glycolysis, Wnt, PARP, HDAC, JAK-STAT, Hedgehog, NOTCH, DNA Repair and Others', or any subgroup thereof of at least 10 intervention points.
 31. A method of treating cancer comprising administering to a patient having cancer a combination of drugs disclosed in Table 6, Table 7, Table 8 or selected from the group consisting of: anti PD1L+Pan RAF inhibitor+MtorPI3K inhibitor; anti PD1L+Pan RAF inhibitor+angiogenesis inhibitor; anti PD1L+Pan RAF inhibitor+MET inhibitor; anti PD1L+Pan RAF inhibitor+CDK4,6 inhibitor; anti CTLA4+Pan RAF inhibitor+MtorPI3K inhibitor; anti CTLA4+Pan RAF inhibitor+angiogenesis inhibitor; anti CTLA4+Pan RAF inhibitor+MET inhibitor; anti CTLA4+Pan RAF inhibitor+CDK4,6 inhibitor; anti PD1L+MEK inhibitor+MtorPI3K dual inhibitor; anti PD1L+MEK inhibitor+angiogenesis inhibitor; anti PD1L+MEK inhibitor+MET inhibitor; anti PD1L+MEK inhibitor+CDK,-6 inhibitor; anti CTLA4+MEK inhibitor+MtorPI3K dual inhibitor; anti CTLA4+MEK inhibitor+MET inhibitor; anti CTLA4+MEK inhibitor+angiogenesis inhibitor; and anti CTLA4+MEK inhibitor+CDK4,6 inhibitor.
 32. The method according to claim 31, wherein the combination of drugs is selected from the group consisting of: Medi-4736+MLN2480+PF-384; Medi-4736+MLN2480+Axitinib or Motesanib; Medi-4736+MLN2480+Crizotinib; Medi-4736+MLN2480+Palbociclib; Tremelimumab+MLN2480+PF-384; Tremelimumab+MLN2480+Axitinib or Motesanib; Tremelimumab+MLN2480+Crizotinib; Tremelimumab+MLN2480+Palbociclib; Medi-4736+Selumetinib+PF-384; Medi-4736+Selumetinib+Axitinib or Motesanib; Medi-4736+Selumetinib+Crizotinib; Medi-4736+Selumetinib+Palbociclib; Tremelimumab+Selumetinib+PF-384; Tremelimumab+Selumetinib+Crizotinib; Tremelimumab+Selumetinib+Axitinib or Motesanib; and Tremelimumab+Selumetinib+Palbociclib. 